Trends Plant Sci , IF:18.313 , 2022 Feb doi: 10.1016/j.tplants.2022.01.008
Transcriptional regulatory network of plant cold-stress responses.
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan. Electronic address: akido@g.ecc.u-tokyo.ac.jp.; Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki 305-0074, Japan.; Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan. Electronic address: akys@g.ecc.u-tokyo.ac.jp.
Recent studies have revealed the complex and flexible transcriptional regulatory network involved in cold-stress responses. Focusing on two major signaling pathways that respond to cold stress, we outline current knowledge of the transcriptional regulatory network and the post-translational regulation of transcription factors in the network. Cold-stress signaling pathways are closely associated with other signaling pathways such as those related to the circadian clock, and large amounts of data on their crosstalk and tradeoffs are available. However, it remains unknown how plants sense and transmit cold-stress signals to regulate gene expression. We discuss recent reports on cold-stress sensing and associated signaling pathways that regulate the network. We also emphasize future directions for developing abiotic stress-tolerant crop plants.
PMID: 35210165
Elife , IF:8.14 , 2022 Feb , V11 doi: 10.7554/eLife.73552
Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter.
The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.; Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.; Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.; Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, Instituto Mexicano del Seguro Social, Mexico City, Mexico.; Swansea University Medical School, Swansea University, Swansea, United Kingdom.; Department of Zoology, University of Oxford, Oxford, United Kingdom.; Department of Medical Sciences, Zoonosis Science Centre, Uppsala University, Uppsala, Sweden.; Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand.
Horizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to transfer to another. This has potential to rapidly promote new adaptive trajectories such as zoonotic transfer or antimicrobial resistance. However, for this to occur requires gaps to align in barriers to recombination within a given time frame. Chief among these barriers is the physical separation of species with distinct ecologies in separate niches. Within the genus Campylobacter, there are species with divergent ecologies, from rarely isolated single-host specialists to multihost generalist species that are among the most common global causes of human bacterial gastroenteritis. Here, by characterizing these contrasting ecologies, we can quantify HGT among sympatric and allopatric species in natural populations. Analyzing recipient and donor population ancestry among genomes from 30 Campylobacter species, we show that cohabitation in the same host can lead to a six-fold increase in HGT between species. This accounts for up to 30% of all SNPs within a given species and identifies highly recombinogenic genes with functions including host adaptation and antimicrobial resistance. As described in some animal and plant species, ecological factors are a major evolutionary force for speciation in bacteria and changes to the host landscape can promote partial convergence of distinct species through HGT.
PMID: 35191377
Genes (Basel) , IF:4.096 , 2022 Feb , V13 (2) doi: 10.3390/genes13020374
Single-Cell Transcriptome and Network Analyses Unveil Key Transcription Factors Regulating Mesophyll Cell Development in Maize.
State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China.; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China.; College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.; Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China.
BACKGROUND: Maize mesophyll (M) cells play important roles in various biological processes such as photosynthesis II and secondary metabolism. Functional differentiation occurs during M-cell development, but the underlying mechanisms for regulating M-cell development are largely unknown. RESULTS: We conducted single-cell RNA sequencing (scRNA-seq) to profile transcripts in maize leaves. We then identified coregulated modules by analyzing the resulting pseudo-time-series data through gene regulatory network analyses. WRKY, ERF, NAC, MYB and Heat stress transcription factor (HSF) families were highly expressed in the early stage, whereas CONSTANS (CO)-like (COL) and ERF families were highly expressed in the late stage of M-cell development. Construction of regulatory networks revealed that these transcript factor (TF) families, especially HSF and COL, were the major players in the early and later stages of M-cell development, respectively. Integration of scRNA expression matrix with TF ChIP-seq and Hi-C further revealed regulatory interactions between these TFs and their targets. HSF1 and COL8 were primarily expressed in the leaf bases and tips, respectively, and their targets were validated with protoplast-based ChIP-qPCR, with the binding sites of HSF1 being experimentally confirmed. CONCLUSIONS: Our study provides evidence that several TF families, with the involvement of epigenetic regulation, play vital roles in the regulation of M-cell development in maize.
PMID: 35205426
BMC Genomics , IF:3.969 , 2022 Feb , V23 (1) : P125 doi: 10.1186/s12864-022-08345-7
Genome-wide identification and expression profiling analysis of maize AP2/ERF superfamily genes reveal essential roles in abiotic stress tolerance.
Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000, China.; Anhui Provincial Key Lab. of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000, China. qyx2011@ahnu.edu.cn.
BACKGROUND: As one of the largest transcription factor families in plants, the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily is involved in various biological processes and plays significant roles in plant growth, development and responses to various stresses. Although identification and characterization of AP2/ERF superfamily genes have been accomplished in many plant species, very little is known regarding the structure and function of AP2/ERF genes in maize. RESULTS: In this study, a total of 214 genes encoding ZmAP2/ERF proteins with complete AP2/ERF domain were eventually identified according to the AGPv4 version of the maize B73 genome. Based on the number of AP2/ERF domain and similarities of amino acid sequences among AP2/ERF proteins from Arabidopsis, rice and maize, all 214 putative ZmAP2/ERF proteins were categorized into three distinct families, including the AP2 family (44), the ERF family (166) and the RAV family (4), respectively. Among them, the ERF family was further subdivided into two diverse subfamilies, including the DREB and ERF subfamilies with 61 and 105 members, respectively. Further, based on phylogenetic analysis, the members of DREB and ERF subfamilies were subdivided into four (Group I-IV) and eight (Group V-XII) groups, respectively. The characteristics of exon-intron structure of these putative ZmAP2/ERF genes and conserved protein motifs of their encoded ZmAP2/ERF proteins were also presented respectively, which was in accordance with the results of group classification. Promoter analysis suggested that ZmAP2/ERF genes shared many stress- and hormone-related cis-regulatory elements. Gene duplication and synteny analysis revealed that tandem or segmental duplication and purifying selection might play significant roles in evolution and functional differentiation of AP2/ERF superfamily genes among three various gramineous species (maize, rice and sorghum). Using RNA-seq data, transcriptome analysis indicated that the majority of ZmAP2/ERF genes displayed differential expression patterns at different developmental stages of maize. In addition, the following analyses of co-expression network among ZmAP2/ERF genes and protein protein interaction between ZmAP2 and ZmERF proteins further enabled us to understand the regulatory relationship among members of the AP2/ERF superfamily in maize. Furthermore, by quantitative real-time PCR analysis, twenty-seven selected ZmAP2/ERF genes were further confirmed to respond to three different abiotic stresses, suggesting their potential roles in various abiotic stress responses. Collectively, these results revealed that these ZmAP2/ERF genes play essential roles in abiotic stress tolerance. CONCLUSIONS: Taken together, the present study will serve to present an important theoretical basis for further exploring the function and regulatory mechanism of ZmAP2/ERF genes in the growth, development, and adaptation to abiotic stresses in maize.
PMID: 35151253
Plants (Basel) , IF:3.935 , 2022 Feb , V11 (4) doi: 10.3390/plants11040510
Metabolic Circuits in Sap Extracts Reflect the Effects of a Microbial Biostimulant on Maize Metabolism under Drought Conditions.
Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa.; International Research and Development Division, Omnia Group, Johannesburg 2021, South Africa.
The use of microbial biostimulants in the agricultural sector is increasingly gaining momentum and drawing scientific attention to decode the molecular interactions between the biostimulants and plants. Although these biostimulants have been shown to improve plant health and development, the underlying molecular phenomenology remains enigmatic. Thus, this study is a metabolomics work to unravel metabolic circuits in sap extracts from maize plants treated with a microbial biostimulant, under normal and drought conditions. The biostimulant, which was a consortium of different Bacilli strains, was applied at the planting stage, followed by drought stress application. The maize sap extracts were collected at 5 weeks after emergence, and the extracted metabolites were analyzed on liquid chromatography-mass spectrometry platforms. The acquired data were mined using chemometrics and bioinformatics tools. The results showed that under both well-watered and drought stress conditions, the application of the biostimulant led to differential changes in the profiles of amino acids, hormones, TCA intermediates, phenolics, steviol glycosides and oxylipins. These metabolic changes spanned several biological pathways and involved a high correlation of the biochemical as well as structural metabolic relationships that coordinate the maize metabolism. The hypothetical model, postulated from this study, describes metabolic events induced by the microbial biostimulant for growth promotion and enhanced defences. Such understanding of biostimulant-induced changes in maize sap pinpoints to the biochemistry and molecular mechanisms that govern the biostimulant-plant interactions, which contribute to ongoing efforts to generate actionable knowledge of the molecular and physiological mechanisms that define modes of action of biostimulants.
PMID: 35214843
Prev Vet Med , IF:2.67 , 2022 Feb , V199 : P105556 doi: 10.1016/j.prevetmed.2021.105556
Preventive effect of on-farm biosecurity practices against highly pathogenic avian influenza (HPAI) H5N6 infection on commercial layer farms in the Republic of Korea during the 2016-17 epidemic: A case-control study.
Veterinary Epidemiology Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea; Department of Public Health, Graduate School, Korea University, Seoul, 02841, Republic of Korea. Electronic address: shanuar@korea.kr.; Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.; Department of Public Health, Graduate School, Korea University, Seoul, 02841, Republic of Korea.; Veterinary Epidemiology Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.; Farm Animal Clinical Training and Research Center, Seoul National University, Pyeongchang, 25354, Republic of Korea.; Department of Computer and Information Science, Korea University, Seojong, 30019, Republic of Korea.
Highly pathogenic avian influenza virus (HPAIv) H5N6 has destructive consequences on the global poultry production system. Recently, a growing number of layer farms have been heavily damaged from the HPAIv epidemic due to the increased virulence of the virus and the intensification of the production system. Therefore, stakeholders should implement effective preventive practices at the farm level that are aligned with contingency measures at the national level to minimize poultry losses. However, numerous biosecurity protocols for layer farm workers to follow have been developed, impeding efficient prevention and control. Furthermore, the effectiveness of biosecurity practices varies with the geographical condition and inter-farm contact structures. Hence, the objective of our study was to examine the preventive effect of five biosecurity actions commonly practiced at layer farms in the Republic of Korea against HPAIv H5N6: (i) fence installation around a farm, ii) rodent control inside a farm; iii) disinfection booth for visitors for disinfection protocols, iv) an anterior room in the sheds before entering the bird area and v) boots changes when moving between sheds in the same farm. We conducted a case-control study on 114 layer case farms and 129 layer control farms during the 2016-17 HPAI epidemic. The odds ratios for five on-farm biosecurity practices implemented in those study groups were estimated as a preventive effect on the HPAI infection with covariates, including seven geographical conditions and three network metrics using Bayesian hierarchical logistic regression and geographical location weighted logistic regression. The results showed that the use of a disinfection booth for personnel reduced the odds of HPAIv H5N6 infection (adjusted odds ratio [AOR] = 0.002, 95 % credible interval [CrI] = 0.00007 - 0.025) with relatively small spatial variation (minimum AOR - maximum AOR: 0.084-0.263). Changing boots between sheds on the same farm reduced the odds of HPAIv H5N6 infection (AOR = 0.160, 95 % CrI = 0.024-0.852) with relatively wide spatial variation (minimum AOR - maximum AOR = 0.270-0.688). Therefore, enhanced personnel biosecurity protocols at the farm of entry for layer farms is recommended to effectively prevent and respond to HPAIv H5N6 infection under different local condition. Our study provides an important message for layer farmers to effectively implement on-farm biosecurity actions against HPAIv H5N6 infection at their farms by setting priorities based on their spatial condition and network position.
PMID: 34896940
J Transp Geogr , 2022 Feb , V99 : P103265 doi: 10.1016/j.jtrangeo.2021.103265
Global shipping network dynamics during the COVID-19 pandemic's initial phases.
Department of Operations and Technology, Kuhne Logistics University (KLU), Hamburg, Germany.
Catastrophic incidents can significantly disrupt supply chains, but most of these disruptions remain localized. It was not until the onset of COVID-19 that a disruption in our lifetimes achieved a global magnitude. In order to contain the pandemic, governments around the world resorted to closing borders, shutting down manufacturing plants, and imposing lockdowns, which resulted in disrupted production capabilities and weakened consumer spending. The effects of these measures have been clearly visible in global transport networks, where disruptions ripple through the system and serve as a precursor to the disruptions in the broader economy. In this study, we use liner shipping schedule cancellations, a form of serious transport network disruption, as distress signals of the pandemic's impact on global supply chains. Our study applies a three-stage approach and provides insights into operator behaviors when under distress. We show that the pandemic challenged service network integrity and that network disruptions first clustered in Asia before rippling along main trade routes. Agile liner shipping operations, aided by planned service suspensions, prevented the collapse of the global maritime transport networks and indicated the maritime industry's ability to withstand even major catastrophic incidents.
PMID: 35035126