Genome-wide identification of heat shock factors and heat shock proteins in response to UV and high intensity light stress in lettuce

Abstract

Background Heat shock factors (Hsfs) and Heat shock proteins (Hsps) belong to an essential group of molecular regulators involved in controlling cellular processes under normal and stress conditions. The role of Hsfs and Hsps is well known in model plant species under diverse stress conditions. While plants Hsfs are vital components of the signal transduction response to maintain cellular homeostasis, Hsps function as chaperones helping to maintain folding of damaged and newly formed proteins during stress conditions. In lettuce (Lactuca sativa), a highly consumed vegetable crop grown in the field and in hydroponic systems, the role of these gene families in response to artificial light is not well characterized. Results Using a genome-wide analysis approach, we identified 32 Hsfs and 22 small heat shock proteins (LsHsps) in lettuce, some of which do not have orthologs in Arabidopsis, poplar, and rice. LsHsp60s, LsHsp90s, and LsHsp100s are highly conserved among dicot and monocot species. Surprisingly, LsHsp70s have three times more members than Arabidopsis and two times more than rice. Interestingly, the lettuce genome triplication did not contribute to the increased number of LsHsp70s genes. The large number of LsHsp70s was the result of genome tandem duplication. Chromosomal distribution analysis shows larger tandem repeats of LsHsp70s genes in Chr1, Chr7, Chr8, and Chr9. At the transcriptional level, some genes of the LsHsfs, LsHsps, LsHsp60s, and LsHsp70s families were highly responsive to UV and high intensity light stress, in contrast to LsHsp90s and LsHsp100s which did not respond to a light stimulus. Conclusions Our genome-wide analysis provides a detailed identification of Hsfs and Hsps in lettuce. Chromosomal location and syntenic region analysis together with our transcriptional analysis under different light conditions provide candidate genes for breeding programs aiming to produce lettuce varieties able to grow healthy under hydroponic systems that use artificial light.

ScRpb4, Encoding an RNA Polymerase Subunit from Sugarcane, Is Ubiquitously Expressed and Resilient to Changes in Response to Stress Conditions

“…It remains unknown whether these extra copies of Rpb4 in Setaria italica are, in fact, functional genes or, in contrast, nonfunctional copies. In lettuce, for instance, genome triplication did not contribute to the increased gene number of LsHsp70s genes or LsHsfs [26]. Therefore, the increased number of Rpb4 genes in Setaria italica could be due to another evolutionary mechanism.…”

“…Wholegenome duplications and triplications have been suggested as the drivers of the increased gene members [45,46]. However, these assumptions do not apply to all gene families [26]. Therefore, an extensive survey is necessary to pinpoint whether the increased number of Rpb4 in some monocotyledonous and dicotyledonous is an adaptative response to environmental cues or the result of whole-genome gene duplications or triplications.…”

“…RNA polymerase II subunit IV (Rpb4) sequences from plants (monocots, dicots, and bryophytes), animals, and fungi were retrieved from public databases. When a gene had splice variants, primary transcripts were selected as representative for the gene [26]. The retrieved sequences were used as queries in an automated BLASTP search against all the genomes available in Phytozome [27].…”

“…One of the most common consequences of stress exposure in plants is a transcriptional disruption [18,19,21,22,26]. Since ScRpb4 is a putative member of the transcriptional machinery in sugarcane, we tested ScRpb4's transcriptional response to a variety of stress conditions.…”

De novo Whole-Genome Assembly of Moringa oleifera Helps Identify Genes Regulating Drought Stress Tolerance

“…Z. et al, 2020 ). They are a relatively small family of TFs with 22 and 25 members reported in Arabidopsis and rice, respectively ( Guo et al, 2008 ), 38 HSFs in soybean ( Li et al, 2014 ), 16 and 17 HSFs, respectively, in two species of wild peanuts ( Wang et al, 2017 ), 33 HSFs in radish ( Tang et al, 2019 ), and 32 HSFs in lettuce ( Kim et al, 2021 ). We identified 21 putative HSFs in the genome of M. oleifera and divided them into three classes based on the structure of the HR-A/B domain that is responsible for the protein interaction activity of HSFs ( Scharf et al, 2012 ).…”