Identification and analysis of regulatory elements in the germin and germin-like proteins family promoters in rice

Abstract

IntroductionGermins and germin-like proteins (GLPs) belong to the cupin superfamily of proteins, identified in several plants, including monocot, dicot, gymnosperms, Physarum polycephalum, and myxomycete (slime mold), after initial discovery of a protein marker germin in the germination of wheat seeds. Germin relatives have also been recognized in animals, prokaryotes, and fern spores (Lu et al., 2010).Germins and GLPs present major problems in classification due to their high sequence conservation in multiple plant species (Dunwell and Gane, 1998). A strong classification system is established by structural characteristics of these proteins due to the clustering of proteins with conserved functions (Agarwal et al., 2009). The proteins that have oxalate oxidase (OXO) enzymes activity, exclusively found within cereal plant species, are placed in a well-conserved homogeneous group called true germins (Carrillo et al., 2009;Davidson et al., 2009), while the germin-motif comprising proteins with an average of 50% amino acid sequence identity that either do not have OXO action or have not yet been allotted an enzymatic function are placed in a heterogeneous group called germinlike protein (Dunwell et al., 2008;Breen and Bellgard, 2010).To date, major research on germins and GLPs has been conducted on cereal plants, especially wheat, maize, barley, and rice. On the basis of various enzymatic activities, six germin subfamilies (GER1-6) have been described. GER1 (true germin proteins) has been shown to possess OXO activity, while GER2 has been shown to possess superoxide dismutase (SOD) action (Banerjee and Maiti, 2010). It has also been shown that the GER1 subfamily is important for early plant development and germination in plants (Federico et al., 2006). The GLPs with mostly unknown function in plant genomes have been classified into subfamilies Thornburg, 1999, 2000). In contrast to a true germin subfamily, both GLP1 and GLP2 subfamilies are limited to proteins of SOD action, while GLP3 is involved in phosphodiesterase activities. However, recently more subdivisions were suggested (Breen and Bellgard, 2010). A key feature of the germin and GLP subdivisions was the conservation of a motif derived from that of the cupin superfamily (Carter and Thornburg,

RETRACTED: Biosynthesis and characterization of iron oxide nanoparticles from Mentha spicata and screening its combating potential against Phytophthora infestans

“…Phytophthora infestans is one of the important phytopathogen causing diseases to the solanaceae species, mainly potato ( Solanum tuberosum ) and tomato ( Solanum lycopersicum ; Nowicki et al, 2012 ). P. infestans belongs to the pathogenic class of oomycetes that effecting the growth of important vegetable crops ( Kim and Judelson, 2003 ; Ali et al, 2015 ; Ali and Mahmood, 2015 ). P. infestans is one of the most aggressive pathogens due to its high adaptability to the host plant ( Ivanov et al, 2021 ).…”

In silico analysis of transcription factor binding sites in promoters of germin-like protein genes in rice

“…Phylogenetic analysis of 43 OsGLP gene promoters revealed a narrow genetic background (0.2%), suggest-ing a high similarity that is smaller than the reported value of 31% [24] for seven GLP promoters from different plant species, but concurs with the previous report [25] in which 44 GLP promoters mostly from rice were considered. This could be due to the fact that in our analysis all of the promoters belong to the same species (Oryza sativa ssp.…”

“…In rice, in silico analysis of OsRGLP1 [22], Os-RGLP2 [23] and 52GLP gene promoters from various plant species including rice [24,25] has predicted the existence of numerous TFBSs that participate in responses to wounding, dehydration, light responsiveness, dark-induced senescence, stresses (pathogen and salt), pollen-specific expression, plant growth regulators and elements related to seed storage proteins, etc., with the roles of OsRGLP2 in the response to wounding, dehydration stress and pathogenicity confirmed [26,27]. Thus far, no comprehensive study has been conducted on rice GLPs promoters, TFBSs and their putative roles in various processes that could predict their functioning.…”

Molecular Characterization of Germin-like Protein Genes in Zea mays (ZmGLPs) Using Various In Silico Approaches

“…GLPs can be found in all plant groups with their number varying greatly among different plant species. 3 Till now, around 254 GLP genes have been reported in almost 53 plant species from numerous databases 4 with their number constantly increasing with a recent report of 350. 5 Many of them have been confirmed for providing potential resistance against various biotic and abiotic stresses.…”