The ORFans’ tale: new insights in plant biology

• Published in: Trends in plant science 2023-12, Vol.28 (12), p.1379-1390
• Main Authors: Fakhar, Ali Zeeshan, Liu, Jinbao, Pajerowska-Mukhtar, Karolina M., Mukhtar, M. Shahid
• Format: Article
• Language: English
• Subjects: cross-species transfer; functional analysis; gene transfer; genetically modified organisms; immunity; immunomodulation; metabolism; molecular/mechanistic events; Orphan Genes; plant hormones; protein kinases; rapamycin; reproduction; sequence homology; SnRK–TOR axis; species; stress biology; sucrose
• ISSN: 1360-1385; 1878-4372
• DOI: 10.1016/j.tplants.2023.06.011

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. 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. Orphan genes (OGs) are taxonomically restricted, without significant sequence similarities to closely related species; they might have evolved from noncoding sequences via rearrangements or duplication and divergence.OGs from divergent species can interact with conserved regulators – such as sucrose non-fermenting 1 (SNF1)-related protein kinases (SnRKs), nuclear factor Y subunit C4 (NF-YC4) – and display the evolutionarily conserved functions.OGs have been shown to promote growth and development in the carbon metabolism of plants, possibly through the target of rapamycin (TOR)–SnRK1 signaling a