Transcriptome Dynamics of Common Bean Roots Exposed to Various Heavy Metals Reveal Valuable Target Genes and Promoters for Genetic Engineering

Understanding the gene regulatory basis of plant response
to heavy
metals (HMs) is fundamental for the management of food safety and
security. However, a comprehensive and comparative view of the plant
responses to different HMs is still lacking. Here, we compared root
transcriptomes in common bean under 9 HM treatments at 50 μM
for three time points each. Cd, Cr, Co, Ni, and Pb caused most severe
morphological and/or biochemical retardations. A total of 448 genes
were found to be responsive to all nine HMs, which were mostly involved
in photosynthesis, oxidization–reduction, and ion binding.
Cd and Cu triggered the greatest number of unique differentially expressed
genes (DEG)s, which were predominantly related to cellular transport/localization
in the former and RNA binding in the latter. Short-term and prolonged
HM treatments shaped very different DEG patterns. Weighted gene co-expression
network analysis identified six co-expression modules showing exceptionally
high transcripts abundance in specific HM × time scenarios. We
experimentally verified the promoter activity of the gene GIP1 and the novel function of XTH23 under
Cu/Cd stress. Collectively, the transcriptomic atlas provides valuable
resources for better understanding the common and unique mechanisms
of plant response to different HMs and offers a mass of candidate
target genes/promoters for genetic engineering.