A TIReless battle: TIR domains in plant-pathogen interactions

The ORFans' tale: new insights in plant biology

Orphan genes (OGs) are protein-coding genes without a significant sequence similarity in closely related species. Despite their functional importance, very little is known about the underlying molecular mechanisms by which OGs participate in diverse biological processes. Here, we discuss the evolutionary mechanisms of OGs' emergence with relevance to species-specific adaptations. We also provide a mechanistic view of the involvement of OGs in multiple processes, including growth, development, reproduction, and carbon-metabolism-mediated immunity. We highlight the interconnection between OGs and the sucrose nonfermenting 1 (SNF1)-related protein kinases (SnRKs)-target of rapamycin (TOR) signaling axis for phytohormone signaling, nutrient metabolism, and stress responses. Finally, we propose a high-throughput pipeline for OGs' interspecies and intraspecies gene transfer through a transgenic approach for future biotechnological advances.

The Lost and Found: Unraveling the Functions of Orphan Genes

Orphan Genes (OGs) are a mysterious class of genes that have recently gained significant attention. Despite lacking a clear evolutionary history, they are found in nearly all living organisms, from bacteria to humans, and they play important roles in diverse biological processes. The discovery of OGs was first made through comparative genomics followed by the identification of unique genes across different species. OGs tend to be more prevalent in species with larger genomes, such as plants and animals, and their evolutionary origins remain unclear but potentially arise from gene duplication, horizontal gene transfer (HGT), or de novo origination. Although their precise function is not well understood, OGs have been implicated in crucial biological processes such as development, metabolism, and stress responses. To better understand their significance, researchers are using a variety of approaches, including transcriptomics, functional genomics, and molecular biology. This review offers a comprehensive overview of the current knowledge of OGs in all domains of life, highlighting the possible role of dark transcriptomics in their evolution. More research is needed to fully comprehend the role of OGs in biology and their impact on various biological processes.

A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions

Investigating the complexity of host-pathogen interactions is challenging. Here, we outline a pipeline to identify important proteins and signaling molecules in human-viral interactomes. Firstly, we curate a comprehensive human interactome. Subsequently, we infer viral targets and transcriptome-specific human interactomes (VTTSHI) for papillomavirus and herpes viruses by integrating viral targets and transcriptome data. Finally, we reveal the common and shared nodes and pathways in viral pathogenesis following network topology and pathway enrichment analyses.

For complete details on the use and execution of this protocol, please refer to Kumar et al. (2020).

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Protocol for integrative analysis of transcriptome and proteome network data

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Network subgroup enrichment of two host-pathogen interaction networks

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Preprocessing of data and heterogeneous network integration

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.