Coevolutionary insights between promoters and transcription factors in the plant and animal kingdoms

Zhang, Jingsong; Wang, Hai-Quan; Xia, Jie; Sha, Kun; He, Shuangchi; Dai, Hao; Hao, Xiaohu; Zhou, Yiwei; Wang, Qiu; Ding, Keke; Ju, Zhang-Lei; Wang, Wen; Chen, Luonan

doi:10.24272/j.issn.2095-8137.2022.111

Cited by 3 publications

(1 citation statement)

References 38 publications

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“…Our study (Figures 6, 7) showed that DDIs can be further studied and used for PPI analysis. However, factors such as domain sequence variations, interaction interface differences, promoters and transcription factors (97), and general host environmental conditions may also influence PPIs and disease outcomes. Furthermore, experimental results may also vary in apparently similar experimental designs (98)(99)(100).…”

Section: Discussion and Future Workmentioning

confidence: 99%

A new framework for host-pathogen interaction research

Huffman

et al. 2022

Front. Immunol.

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COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed.

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Section: Discussion and Future Workmentioning

confidence: 99%

A new framework for host-pathogen interaction research

Huffman

et al. 2022

Front. Immunol.

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Detecting dynamical causality by intersection cardinal concavity

Tao¹,

Wang²,

Shi³

et al. 2023

Fundamental Research

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Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by Penicillium digitatum

Yin

Han

et al. 2023

CIMB

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WRKY transcription factors (TFs) play a vital role in plant stress signal transduction and regulate the expression of various stress resistance genes. Sweet orange (Citrus sinensis) accounts for a large proportion of the world’s citrus industry, which has high economic value, while Penicillium digitatum is a prime pathogenic causing postharvest rot of oranges. There are few reports on how CsWRKY TFs play their regulatory roles after P. digitatum infects the fruit. In this study, we performed genome-wide identification, classification, phylogenetic and conserved domain analysis of CsWRKY TFs, visualized the structure and chromosomal localization of the encoded genes, explored the expression pattern of each CsWRKY gene under P. digitatum stress by transcriptome data, and made the functional prediction of the related genes. This study provided insight into the characteristics of 47 CsWRKY TFs, which were divided into three subfamilies and eight subgroups. TFs coding genes were unevenly distributed on nine chromosomes. The visualized results of the intron-exon structure and domain are closely related to phylogeny, and widely distributed cis-regulatory elements on each gene played a global regulatory role in gene expression. The expansion of the CSWRKY TFs family was probably facilitated by twenty-one pairs of duplicated genes, and the results of Ka/Ks calculations indicated that this gene family was primarily subjected to purifying selection during evolution. Our transcriptome data showed that 95.7% of WRKY genes were involved in the transcriptional regulation of sweet orange in response to P. digitatum infection. We obtained 15 differentially expressed genes and used the reported function of AtWRKY genes as references. They may be involved in defense against P. digitatum and other pathogens, closely related to the stress responses during plant growth and development. Two interesting genes, CsWRKY2 and CsWRKY14, were expressed more than 60 times and could be used as excellent candidate genes in sweet orange genetic improvement. This study offers a theoretical basis for the response of CSWRKY TFs to P. digitatum infection and provides a vital reference for molecular breeding.

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Coevolutionary insights between promoters and transcription factors in the plant and animal kingdoms

Cited by 3 publications

References 38 publications

A new framework for host-pathogen interaction research

A new framework for host-pathogen interaction research

Detecting dynamical causality by intersection cardinal concavity

Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by Penicillium digitatum

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