StAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication.

Sanjeet Kumar Mahtha,Ravi Kiran Purama,Gitanjali Yadav

doi:10.3389/fgene.2021.737194

Abstract

The StAR-related lipid transfer (START) domain containing proteins or START proteins, encoded by a plant amplified family of evolutionary conserved genes, play important roles in lipid binding, transport, signaling, and modulation of transcriptional activity in the plant kingdom, but there is limited information on their evolution, duplication, and associated sub- or neo-functionalization. Here we perform a comprehensive investigation of this family across the rice pangenome, using 10 wild and cultivated varieties. Conservation of START domains across all 10 rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication and domain structure patterns. Analysis of synteny highlights a preponderance of segmental and dispersed duplication among STARTs, while transcriptomic investigation of the main cultivated variety Oryza sativa var. japonica reveals sub-functionalization amongst genes family members in terms of preferential expression across various developmental stages and anatomical parts, such as flowering. Ka/Ks ratios confirmed strong negative/purifying selection on START family evolution, implying that ontogeny recapitulated selection pressures during rice domestication. Our findings provide evidence for high conservation of START genes across rice varieties in numbers, as well as in their stringent regulation of Ka/Ks ratio, and showed strong functional dependency of plants on START proteins for their growth and reproductive development. We believe that our findings advance the limited knowledge about plant START domain diversity and evolution, and pave the way for more detailed assessment of individual structural classes of START proteins among plants and their domain specific substrate preferences, to complement existing studies in animals and yeast.

Highlights

The steroidogenic acute regulatory protein (StAR) related lipid transfer (START) domain was initially identified and named after mammalian StAR protein of 30 kDa, which binds to cholesterol (Stocco, 2001)
The breakup of these StAR-related lipid transfer (START) domains, in terms of potential functions based on domain combinations, is explored further but these general numbers suggest that the increase in START domains among cultivated rices, may reflect an evolving role of STARTs in stress induction or stress response
The START domains are abundant in plants and play a crucial role in plant physiology and development

Summary

Introduction

The steroidogenic acute regulatory protein (StAR) related lipid transfer (START) domain was initially identified and named after mammalian StAR protein of 30 kDa, which binds to cholesterol (Stocco, 2001). Comparative Genomics of START Domains amino acids (Tsujishita and Hurley, 2000) and play a crucial role in the transfer of lipids/sterols, lipid signaling, and modulation of transcription activity (Ponting and Aravind, 1999; Soccio and Breslow, 2003). Presence of START domains across evolutionarily distant organisms indicates a conserved mechanism for proteinlipid/sterol interaction through hydrophobic pockets (Iyer et al, 2001). 21 of the 90 HD family members identified in Arabidopsis possess START domains along with putative leucine zippers (Riechmann, 2002). Of these 21, 5 are from class III HD-ZIP subfamily and 16 are from class IV HD-ZIP subfamily (Schrick et al, 2004; Ariel et al, 2007)

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