Searching for an Identity: Functional Characterization of Taxonomically Restricted Genes in Grain Amaranth

Identification of genetic and biochemical mechanisms associated with heat shock and heat stress adaptation in grain amaranths

“…This study also expanded the information regarding the stressresponsive nature of various grain amaranth unknown function genes reported in prior studies (Deĺano-Frier et al, 2011;Cabrales-Orona and Deĺano-Frier, 2021). Thus, WDS was found to induce the expression of AhHAB4-PAI-1, AhBAMY and AhTIL, which reached their highest levels at an intermediate stage of the WDS treatment applied, whereas these genes, except AhBAMY, were mostly unsensitive to high salt stress.…”

“…The criteria used to select the genes tested were the following: 1) Previous experimental evidence of their induced expression in response to several (a)biotic stress conditions in grain amaranth ( Délano-Frier et al., 2011 ) and other plants, and 2) presumable participation in the regulation and/or responses designed to protect plants from heat-related stress conditions. The analysis included AhHAB4-PAI-1 (Phytozome 13, v2.1, accession number: AH018279) coding for an RNA- and hyaluronan-binding protein; AhRIP (Phytozome 13, v2.1, accession number: AH007263) coding for an RNA-editing factor interacting protein involved in chloroplast and mitochondrial RNA editing, similar to a protein recently found to participate in mitochondrial development in salt-stressed A. thaliana ( Jiang et al., 2021 ); Ah2880 (Phytozome 13, v2.1, accession number: AH015341) coding for a small unknown function protein that, similarly to AhRIP , was shown to be differentially induced in grain amaranths by various biotic and abiotic stress conditions ( Délano-Frier et al., 2011 ; Cabrales-Orona and Délano-Frier, 2021 ); AhBAMY (Phytozome 13, v2.1, accession number: AH001114), coding for a β-amylase that was shown to provide heat stress-resistance when over-expressed in A. thaliana ( Cabrales-Orona, 2016 ); AhDGR2 (Phytozome 13, v2.1, accession number: AH015369) coding for a DUF642 protein that altered root growth and cell wall structure when overexpressed in transgenic A. thaliana plants ( Palmeros-Suárez et al., 2017 ); AhTIL (Phytozome 13, v2.1, accession number: AH014131) coding for a temperature-induced lipocalin, similar to proteins known to provide thermo-tolerance in A. thaliana ( Chi et al., 2009 ); AhERD (Phytozome 13, v2.1, accession number: AH006452), coding for a senescence/dehydration-associated protein similar to EARLY RESPONSIVE TO DEHYDRATION 7, ERD7, one of several proteins identified in lipid droplets, i,e. neutral-lipid-containing organelles isolated from drought-stressed A. thaliana leaves ( Doner et al., 2021 ), and AhOEE (Phytozome 13, v2.1, accession number: AH015200), coding for an oxygen evolving enhancer protein found to be strongly affected by (a)biotic stresses in A. hypochondriacus ( Délano-Frier et al., 2011 ).…”

“…This resilience has been associated with various anatomical, physiological and biochemical adaptations ( 2014 ; 2015 ; Miller et al., 1984 ; Lal and Edwards, 1996 ; Brenner et al., 2000 ; Johnson and Henderson, 2002 ; Délano-Frier et al., 2004 ; Liu and Stützel, 2004 ; Sánchez-Hernández et al., 2004 ; Omami and Hammes, 2006 ; Omamt et al., 2006 ; Aguilar-Hernández et al., 2011 ; Huerta-Ocampo et al., 2011 ; Caselato-Sousa and Amaya-Farfán, 2012 ; Castrillón-Arbeláez et al., 2012 ; Vargas-Ortiz et al., 2013 ; Vargas-Ortiz et al, 2015 ; Casarrubias-Castillo et al., 2014 ; González-Rodríguez et al., 2019 ; Jamalluddin et al., 2019 ; Cisneros-Hernández et al., 2021 ). Additional data from a large-scale transcriptomic analysis of A. hypochondriacus plants revealed the presence several orphan or unknown function genes that changed their expression levels in response to diverse stress conditions ( Délano-Frier et al., 2011 ), a number of which were found to significantly increase (a)biotic stress tolerance when over-expressed in Arabidopsis thaliana ( Massange-Sánchez et al, 2015 ; Massange-Sánchez et al, 2016 ; Palmeros-Suárez et al, 2015 ; Palmeros-Suárez et al, 2017 ; Cabrales-Orona, 2016 ; Cabrales-Orona, 2017 ; Cabrales-Orona, 2016 ; Cabrales-Orona, 2017 ; Cabrales-Orona and Délano-Frier, 2021 ; Cabrales-Orona et al., 2022 ).…”

Research Advances and Prospects of Orphan Genes in Plants

“…Studies have also described a unique set of TRGs present in grain amaranths, a characteristic feature that can be crucial for maintaining a high level of stress tolerance in a variety of conditions (Cabrales-Orona and Délano-Frier, 2021). In parallel, BRB (Big Root Biomass) is a Lamiales-specific gene, the overexpression of BRB in Arabidopsis modulates root and shoot traits whereas the same gene has been found responsible to induce drought stress sensitivity, modulating the auxin pathway along with a major impact on root and shoot traits (Dossa et al, 2021).…”

Functional Characterization of an Amaranth Natterin-4-Like-1 Gene in Arabidopsis thaliana

“…A transcriptomic analysis of A. hypochondriacus plants subjected to diverse stress conditions further revealed that a substantial number of the genes that underwent changes in expression levels were orphan genes or had unknown function (Délano-Frier et al, 2011). Subsequent over-expression of a number of these genes in Arabidopsis thaliana suggested their participation in diverse mechanisms utilized by Amaranthus plant species to thrive in unfavorable environmental conditions (Massange-Sanchez et al, 2015;Massange-Sánchez et al, 2016;Palmeros-Suárez et al, 2015, 2017Cabrales-Orona, 2017;Cabrales-Orona and Délano, 2021).…”