Proc Natl Acad Sci U S A , IF:11.205 , 2022 Jan , V119 (2) doi: 10.1073/pnas.2109995119
Disentangling direct from indirect relationships in association networks.
Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019.; Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019.; Glomics Inc., Norman, OK 73072.; Data Science and Biotechnology Institute, Gladstone Institutes, University of California, San Francisco, CA 94158.; Chan Zuckerberg Biohub, San Francisco, CA 94158.; Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94704.; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.; Office of Research and Graduate Studies, Utah State University, Logan, UT 84322.; Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94704; mkfstone@berkeley.edu jzhou@ou.edu.; Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019; mkfstone@berkeley.edu jzhou@ou.edu.; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94705.; School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019.
Networks are vital tools for understanding and modeling interactions in complex systems in science and engineering, and direct and indirect interactions are pervasive in all types of networks. However, quantitatively disentangling direct and indirect relationships in networks remains a formidable task. Here, we present a framework, called iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity), for quantitatively inferring direct dependencies in association networks. Using copula-based transitivity, iDIRECT eliminates/ameliorates several challenging mathematical problems, including ill-conditioning, self-looping, and interaction strength overflow. With simulation data as benchmark examples, iDIRECT showed high prediction accuracies. Application of iDIRECT to reconstruct gene regulatory networks in Escherichia coli also revealed considerably higher prediction power than the best-performing approaches in the DREAM5 (Dialogue on Reverse Engineering Assessment and Methods project, #5) Network Inference Challenge. In addition, applying iDIRECT to highly diverse grassland soil microbial communities in response to climate warming showed that the iDIRECT-processed networks were significantly different from the original networks, with considerably fewer nodes, links, and connectivity, but higher relative modularity. Further analysis revealed that the iDIRECT-processed network was more complex under warming than the control and more robust to both random and target species removal (P < 0.001). As a general approach, iDIRECT has great advantages for network inference, and it should be widely applicable to infer direct relationships in association networks across diverse disciplines in science and engineering.
PMID: 34992138
Bioresour Technol , IF:9.642 , 2022 Jan , V347 : P126724 doi: 10.1016/j.biortech.2022.126724
Simultaneously advanced removal of nitrogen and phosphorus in a biofilter packed with ZVI/PHBV/sawdust composite: Deciphering the succession of dominant bacteria and keystone species.
Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.; Department of Environmental Science, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; The Key Laboratory of Water and Sediment Sciences (Peking University), Ministry of Education, Beijing 100871, China. Electronic address: wzwu@pku.edu.cn.
In this study, a biofilter was developed with a ZVI/PHBV/sawdust (ZPS) composite for treating simulative secondary effluent from wastewater treatment plants. Results showed that effluent concentrations of NO3(-)-N and TP in the ZPS biofilter were stable below 2.0 mg/L and 0.1 mg/L, corresponding to 95% NO3(-)-N removal and 99% TP removal, respectively. Microbial community analysis revealed that the transformation of dominant taxa from Dechloromonas to Clostridium sensu stricto_7 from 30 d to 120 d suggested that the ZVI-induced succession of dominant fermentation bacteria ensured the stable carbon supply for denitrification. Co-occurrence network analysis showed that the ZVI directly enhanced the interaction of microbial community. Fe-related bacteria occupied a key position in the rare species, which might maintain the function of iron-mediated organic matter decomposition and denitrification. These findings provide an alternative for advanced removal of nitrogen and phosphorus in biofilters packed with ZPS composites.
PMID: 35065223
J Exp Bot , IF:6.992 , 2022 Jan , V73 (1) : P110-122 doi: 10.1093/jxb/erab399
A gene regulatory network for tiller development mediated by Tin8 in maize.
National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China.
The complex gene regulatory network underlying tiller development in maize remains largely unknown. Here we identified two major quantitative trait loci for tiller number, Tin8 on chromosome 8 and the previously known Tb1 on chromosome 1, in a population derived from a teosinte-maize cross. Map-based cloning and association mapping revealed that Tin8, corresponding to Zcn8 encoding a phosphatidylethanolamine-binding-related kinase, is down-regulated in transcription, which results in decreased tiller number. A strong interaction between Tin8 and the key gen Tb1 was detected for tiller number. Further RNA-seq analysis showed that the expression of 13 genes related to tiller development was controlled by Tin8. Our results support the existence of a complex gene regulatory network for the outgrowth of the tiller bud in maize, in which Zcn8 controls 13 tiller-related genes, including four genes for hormonal responses. In particular, Zcn8 represses Gt1, D14, and Tru1 through the interaction with Tb1.
PMID: 34453433
Hortic Res , IF:6.793 , 2022 Jan doi: 10.1093/hr/uhab087
Integrative analysis of the shikonin metabolic network identifies new gene connections and reveals evolutionary insight into shikonin biosynthesis.
Department of Horticulture and Landscape Architecture, Purdue University, Indiana 47907.; Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907.; Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907.; Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907.
Plant specialized 1,4-naphthoquinones present a remarkable case of convergent evolution. Species across multiple discrete orders of vascular plants produce diverse 1,4-naphthoquinones via one of several pathways using different metabolic precursors. Evolution of these pathways was preceded by events of metabolic innovation and many appear to share connections with biosynthesis of photosynthetic or respiratory quinones. Here, we sought to shed light on the metabolic connections linking shikonin biosynthesis with its precursor pathways and on the origins of shiknoin metabolic genes. Downregulation of Lithospermum erythrorhizon geranyl diphosphate synthase (LeGPPS), recently shown to have been recruited from a cytoplasmic farnesyl diphosphate synthase (FPPS), resulted in reduced shikonin production and a decrease in expression of mevalonic acid and phenylpropanoid pathway genes. Next, we used LeGPPS and other known shikonin pathway genes to build a coexpression network model for identifying new gene connections to shikonin metabolism. Integrative in silico analyses of network genes revealed candidates for biochemical steps in the shikonin pathway arising from Boraginales-specific gene family expansion. Multiple genes in the shikonin coexpression network were also discovered to have originated from duplication of ubiquinone pathway genes. Taken together, our study provides evidence for transcriptional crosstalk between shikonin biosynthesis and its precursor pathways, identifies several shikonin pathway gene candidates and their evolutionary histories, and establishes additional evolutionary links between shikonin and ubiquinone metabolism. Moreover, we demonstrate that global coexpression analysis using limited transcriptomic data obtained from targeted experiments is effective for identifying gene connections within a defined metabolic network.
PMID: 35048120
Biology (Basel) , IF:5.079 , 2022 Jan , V11 (1) doi: 10.3390/biology11010095
Presence of a Mitovirus Is Associated with Alteration of the Mitochondrial Proteome, as Revealed by Protein-Protein Interaction (PPI) and Co-Expression Network Models in Chenopodium quinoa Plants.
Laboratory of Proteomics and Metabolomics, Institute for Biomedical Technologies (ITB), Department of Biomedical Sciences, National Research Council (CNR), 20054 Milan, Italy.; Institute for Sustainable Plant Protection, Department of Bio-Food Sciences, National Research Council (CNR), 10135 Turin, Italy.; Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, 10135 Turin, Italy.
Plant mitoviruses belong to Mitoviridae family and consist of positive single-stranded RNA genomes replicating exclusively in host mitochondria. We previously reported the biological characterization of a replicating plant mitovirus, designated Chenopodium quinoa mitovirus 1 (CqMV1), in some Chenopodium quinoa accessions. In this study, we analyzed the mitochondrial proteome from leaves of quinoa, infected and not infected by CqMV1. Furthermore, by protein-protein interaction and co-expression network models, we provided a system perspective of how CqMV1 affects mitochondrial functionality. We found that CqMV1 is associated with changes in mitochondrial protein expression in a mild but well-defined way. In quinoa-infected plants, we observed up-regulation of functional modules involved in amino acid catabolism, mitochondrial respiratory chain, proteolysis, folding/stress response and redox homeostasis. In this context, some proteins, including BCE2 (lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex), DELTA-OAT (ornithine aminotransferase) and GR-RBP2 (glycine-rich RNA-binding protein 2) were interesting because all up-regulated and network hubs in infected plants; together with other hubs, including CAT (catalase) and APX3 (L-ascorbate peroxidase 3), they play a role in stress response and redox homeostasis. These proteins could be related to the higher tolerance degree to drought we observed in CqMV1-infected plants. Although a specific causative link could not be established by our experimental approach at this stage, the results suggest a new mechanistic hypothesis that demands further in-depth functional studies.
PMID: 35053093
Plant Dis , IF:4.438 , 2022 Jan doi: 10.1094/PDIS-09-21-1974-RE
Differential microbial communities in paddy soils between Guiyang plateaus and Chengdu basins drive the incidence of rice bacterial diseases.
Chinese Academy of Agricultural Sciences Institute of Plant Protection, 243827, Plant Pathology, Beijing, Beijing, China; yajiaowang515@163.com.; Beijing, China; 454497560@qq.com.; Beijing, China; wnztdr810@126.com.; Beijing, China; liuwenwen01@caas.cn.; Beijing, China; lli@ippcaas.cn.; Chinese Academy of Agricultural Sciences Institute of Plant Protection, 243827, Plant Pathology, Beijing, Beijing, China; wangxifeng@caas.cn.
Southwest China has the most complex rice-growing regions in China. With great differences in topography, mainly consisting of basins and plateaus, ecological factors in above region differ greatly. In this study, bulk paddy soils collected from a long-term rice field in Chengdu (basins) and in Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared more than 70% of the dominant genera (abundance > 1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively related with the higher incidence of rice bacterial foot rot in Guiyang, while temperature had a greater effect on soil microbial functions and positively related with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.
PMID: 35021874
Phytopathology , IF:4.025 , 2022 Jan : PPHYTO06210275R doi: 10.1094/PHYTO-06-21-0275-R
Host Plant Adaptation Drives Changes in Diaphorina citri Proteome Regulation, Proteoform Expression, and Transmission of 'Candidatus Liberibacter asiaticus', the Citrus Greening Pathogen.
U.S. Department of Agriculture-Agricultural Research Service-Emerging Pests and Pathogens Research Unit, Ithaca, NY.; U.S. Department of Agriculture-Agricultural Research Service, USHRL-SIRU, Fort Pierce, FL.; Boyce Thompson Institute for Plant Research, Ithaca, NY.; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.; University of Washington-Genome Sciences, Seattle, WA.; Cornell University College of Agriculture and Life Sciences-Plant Pathology and Plant Microbe Biology, Ithaca, NY.; U.S. Department of Agriculture-Agricultural Research Service-Plant, Soil, and Nutrition Research Unit, Ithaca, NY.
The Asian citrus psyllid (Diaphorina citri) is a pest of citrus and the primary insect vector of the bacterial pathogen, 'Candidatus Liberibacter asiaticus' (CLas), which is associated with citrus greening disease. The citrus relative Murraya paniculata (orange jasmine) is a host plant of D. citri but is more resistant to CLas compared with all tested Citrus genotypes. The effect of host switching of D. citri between Citrus medica (citron) and M. paniculata plants on the acquisition and transmission of CLas was investigated. The psyllid CLas titer and the proportion of CLas-infected psyllids decreased in the generations after transfer from CLas-infected citron to healthy M. paniculata plants. Furthermore, after several generations of feeding on M. paniculata, pathogen acquisition (20 to 40% reduction) and transmission rates (15 to 20% reduction) in psyllids transferred to CLas-infected citron were reduced compared with psyllids continually maintained on infected citron. Top-down (difference gel electrophoresis) and bottom-up (shotgun MS/MS) proteomics methods were used to identify changes in D. citri protein expression resulting from host plant switching between Citrus macrophylla and M. paniculata. Changes in expression of insect metabolism, immunity, and cytoskeleton proteins were associated with host plant switching. Both transient and sustained feeding on M. paniculata induced distinct patterns of protein expression in D. citri compared with psyllids reared on C. macrophylla. The results point to complex interactions that affect vector competence and may lead to strategies to control the spread of citrus greening disease.
PMID: 34738832
BMC Genomics , IF:3.969 , 2022 Jan , V23 (1) : P8 doi: 10.1186/s12864-021-08197-7
Gene regulation network analyses of pistil development in papaya.
Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fujian, 350002, Fuzhou, China.; The Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. rayming@illinois.edu.
BACKGROUND: The pistil is an essential part of flowers that functions in the differentiation of the sexes and reproduction in plants. The stigma on the pistil can accept pollen to allow fertilization and seed development. Papaya (Carica papaya L.) is a dioecious plant, where female flowers exhibit normal pistil, while the male flowers exhibit aborted pistil at a late stage of pistil development. RESULTS: The developmental stages of papaya pistil were analyzed after first dividing it into slices representing the primordium stage 1 (S1), the pre-meiotic stages S2, post-meiotic stage S3, and the mitotic stage S4. The SS scoring algorithm analysis of genes preferentially expressed at different stages revealed differentially expressed genes between male and female flowers. A transcription factor regulatory network for each stage based on the genes that are differentially expressed between male and female flowers was constructed. Some transcription factors related to pistil development were revealed based on the analysis of regulatory networks such as CpAGL11, CpHEC2, and CpSUPL. Based on the specific expression of genes, constructed a gene regulatory subnetwork with CpAGL11-CpSUPL-CpHEC2 functioning as the core. Analysis of the functionally enriched terms in this network reveals several differentially expressed genes related to auxin/ brassinosteroid signal transduction in the plant hormone signal transduction pathway. At the same time, significant differences in the expression of auxin and brassinosteroid synthesis-related genes between male and female flowers at different developmental stages were detected. CONCLUSIONS: The pistil abortion of papaya might be caused by the lack of expression or decreased expression of some transcription factors and hormone-related genes, affecting hormone signal transduction or hormone biosynthesis. Analysis of aborted and normally developing pistil in papaya provided new insights into the molecular mechanism of pistil development and sex differentiation in dioecious papaya.
PMID: 34983382
BMC Bioinformatics , IF:3.169 , 2022 Jan , V23 (1) : P12 doi: 10.1186/s12859-021-04542-5
Path-level interpretation of Gaussian graphical models using the pair-path subscore.
Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.; Department of Biostatistics and Epidemiology, University of Massachusetts - Amherst, Amherst, MA, USA.; Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA.; Duke Molecular Physiology Institute, Durham, NC, USA.; Duke University School of Medicine, Durham, NC, USA.; Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. dscholtens@northwestern.edu.
BACKGROUND : Construction of networks from cross-sectional biological data is increasingly common. Many recent methods have been based on Gaussian graphical modeling, and prioritize estimation of conditional pairwise dependencies among nodes in the network. However, challenges remain on how specific paths through the resultant network contribute to overall 'network-level' correlations. For biological applications, understanding these relationships is particularly relevant for parsing structural information contained in complex subnetworks. RESULTS: We propose the pair-path subscore (PPS), a method for interpreting Gaussian graphical models at the level of individual network paths. The scoring is based on the relative importance of such paths in determining the Pearson correlation between their terminal nodes. PPS is validated using human metabolomics data from the Hyperglycemia and adverse pregnancy outcome (HAPO) study, with observations confirming well-documented biological relationships among the metabolites. We also highlight how the PPS can be used in an exploratory fashion to generate new biological hypotheses. Our method is implemented in the R package pps, available at https://github.com/nathan-gill/pps . CONCLUSIONS: The PPS can be used to probe network structure on a finer scale by investigating which paths in a potentially intricate topology contribute most substantially to marginal behavior. Adding PPS to the network analysis toolkit may enable researchers to ask new questions about the relationships among nodes in network data.
PMID: 34986802