Dataset Information

In Silico Study of the RSH (RelA/SpoT Homologs) Gene Family and Expression Analysis in Response to PGPR Bacteria and Salinity in Brassica napus.

ABSTRACT: Among several mechanisms involved in the plant stress response, synthesis of guanosine tetra and pentaphosphates (alarmones), homologous to the bacterial stringent response, is of crucial importance. Plant alarmones affect, among others, photosynthetic activity, metabolite accumulation, and nutrient remobilization, and thus regulate plant growth and development. The plant RSH (RelA/SpoT homolog) genes, that encode synthetases and/or hydrolases of alarmones, have been characterized in a limited number of plant species, e.g., Arabidopsis thaliana, Oryza sativa, and Ipomoea nil. Here, we used dry-to-wet laboratory research approaches to characterize RSH family genes in the polyploid plant Brassica napus. There are 12 RSH genes in the genome of rapeseed that belong to four types of RSH genes: 6 RSH1, 2 RSH2, 3 RSH3, and 1 CRSH. BnRSH genes contain 13-24 introns in RSH1, 2-6 introns in RSH2, 1-6 introns in RSH3, and 2-3 introns in the CRSH genes. In the promoter regions of the RSH genes, we showed the presence of regulatory elements of the response to light, plant hormones, plant development, and abiotic and biotic stresses. The wet-lab analysis showed that expression of BnRSH genes is generally not significantly affected by salt stress, but that the presence of PGPR bacteria, mostly of Serratia sp., increased the expression of BnRSH significantly. The obtained results show that BnRSH genes are differently affected by biotic and abiotic factors, which indicates their different functions in plants.

SUBMITTER: Dabrowska GB

PROVIDER: S-EPMC8509286 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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In Silico Study of the RSH (RelA/SpoT Homologs) Gene Family and Expression Analysis in Response to PGPR Bacteria and Salinity in Brassica napus.

Dąbrowska Grażyna B GB Turkan Sena S Tylman-Mojżeszek Wioleta W Mierek-Adamska Agnieszka A

International journal of molecular sciences 20211001 19

Among several mechanisms involved in the plant stress response, synthesis of guanosine tetra and pentaphosphates (alarmones), homologous to the bacterial stringent response, is of crucial importance. Plant alarmones affect, among others, photosynthetic activity, metabolite accumulation, and nutrient remobilization, and thus regulate plant growth and development. The plant RSH (RelA/SpoT homolog) genes, that encode synthetases and/or hydrolases of alarmones, have been charact ...[more]

PMID: 34639007

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Project description:RelA/SpoT Homologue (RSH) proteins, named for their sequence similarity to the RelA and SpoT enzymes of Escherichia coli, comprise a superfamily of enzymes that synthesize and/or hydrolyze the alarmone ppGpp, activator of the "stringent" response and regulator of cellular metabolism. The classical "long" RSHs Rel, RelA and SpoT with the ppGpp hydrolase, synthetase, TGS and ACT domain architecture have been found across diverse bacteria and plant chloroplasts, while dedicated single domain ppGpp-synthesizing and -hydrolyzing RSHs have also been discovered in disparate bacteria and animals respectively. However, there is considerable confusion in terms of nomenclature and no comprehensive phylogenetic and sequence analyses have previously been carried out to classify RSHs on a genomic scale. We have performed high-throughput sensitive sequence searching of over 1000 genomes from across the tree of life, in combination with phylogenetic analyses to consolidate previous ad hoc identification of diverse RSHs in different organisms and provide a much-needed unifying terminology for the field. We classify RSHs into 30 subgroups comprising three groups: long RSHs, small alarmone synthetases (SASs), and small alarmone hydrolases (SAHs). Members of nineteen previously unidentified RSH subgroups can now be studied experimentally, including previously unknown RSHs in archaea, expanding the "stringent response" to this domain of life. We have analyzed possible combinations of RSH proteins and their domains in bacterial genomes and compared RSH content with available RSH knock-out data for various organisms to determine the rules of combining RSHs. Through comparative sequence analysis of long and small RSHs, we find exposed sites limited in conservation to the long RSHs that we propose are involved in transmitting regulatory signals. Such signals may be transmitted via NTD to CTD intra-molecular interactions, or inter-molecular interactions either among individual RSH molecules or among long RSHs and other binding partners such as the ribosome.

Project description:Salinity is one of the most severe abiotic stress in the world. Also, the irrigated lands have been treated with second salinity. Canola is one of the most important industrial crops for oil production all over the world which is affected by salinity. Salt stress causes imbalanced ion hemostasis (Na+ and K+) and interrupted mineral absorption in canola. Also, salinity stress leads to oxidative stress (production and accumulation of reactive oxygen species (ROS). Accumulation of ROS is extremely dangerous and lethal for plants. As a consequence, canola production is reduced under salinity stress. So, a suitable approach should be found to deal with salinity stress and prevent the loss of production oilseed. Plant growth-promoting rhizobacteria (PGPR) can colonize on the plant root surface and alleviate the salt stress effect by providing minerals like nitrogen, phosphate, and potassium. Also, they alleviate salt stress by phytohormones like auxin (IAA), cytokinin (CK), and abscisic acid (ABA). This study focus on physiological parameters like leaf area (LA), root length (RL), shoot length (SL), chlorophyll fluorescence indexes (Fv/Fm and Fv/F0), relative water content (RWC), electrolyte leakage index (ELI), photosynthesis pigments (chlorophyll a, b, and carotenoids), Na+, and K+; and biochemical parameters like malondialdehyde (MDA) content, hydrogen peroxide content (H2O2), total protein content, proline, antioxidant capacity, and antioxidant enzyme activities in canola through the inoculation with Enterobacter sp. S16-3 and Pseudomonas sp. C16-2O. This study showed that LA, RL, SL, chlorophyll fluorescence indexes, RWC were significantly increased and ELI was significantly decreased in bacteria inoculated treatments. Also, MDA, H2O2 were decreased, and antioxidant capacity, proline, and antioxidant enzymes were increased due to inoculation with these bacteria. Besides, the amount of K+ as an index of salinity tolerance significantly increased, and leaf Na+ content was significantly decreased.

Dataset Information

In Silico Study of the RSH (RelA/SpoT Homologs) Gene Family and Expression Analysis in Response to PGPR Bacteria and Salinity in Brassica napus.

Publications

In Silico Study of the <i>RSH</i> (<i>RelA</i>/<i>SpoT</i> Homologs) Gene Family and Expression Analysis in Response to PGPR Bacteria and Salinity in <i>Brassica napus</i>.

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