Phenotypic and transcriptomic analysis reveals early stress responses in transgenic rice expressing Arabidopsis DREB1a

Overexpression of Arabidopsis Dehydration Response Element Binding 1a (DREB1a) is a well-known approach for developing salinity, cold and/or drought stress tolerance. However, understanding of the genetic mechanisms associated with DREB1a expression in rice is generally limited. In this study, DREB1a associated early responses were investigated in a transgenic rice line harboring cold-inducible DREB1a at a gene stacked locus. While the function of other genes in the stacked locus was not relevant to stress tolerance, this study demonstrates DREB1a can be colocalized with other genes for multigenic trait enhancement. As expected, the transgenic lines displayed improved tolerance to salinity stress and water withholding when compared to non-transgenic controls. RNA sequencing and transcriptome analysis showed upregulation of complex transcriptional networks and metabolic reprogramming as DREB1a expression led to the upregulation of multiple transcription factor gene families, suppression of photosynthesis and induction of secondary metabolism. In addition to the detection of previously described mechanisms such as production of protective molecules, potentially novel pathways were also revealed. These include jasmonate, auxin, and ethylene signaling, induction of JAZ and WRKY regulons, trehalose synthesis and polyamine catabolism. These genes regulate various stress responses and ensure timely attenuation of the stress signal. Furthermore, genes associated with heat stress response were downregulated in DREB1a overexpressing lines, suggesting antagonism between heat and dehydration stress pathways. In summary, through a complex transcriptional network, multiple stress signaling pathways are induced by DREB1a that presumably lead to early perception and rapid response towards stress tolerance as well as attenuation of the signal to prevent deleterious effects of the runoff response.

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Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽

10.3390/agriculture11030244 ◽

2021 ◽

Vol 11 (3) ◽

pp. 244

Author(s):

Seung Hee Eom ◽

Tae Kyung Hyun

Keyword(s):

Functional Analysis ◽

Brassica Rapa ◽

Chinese Cabbage ◽

Stress Responses ◽

Histone Deacetylases ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Gene Families ◽

Physiological Processes ◽

Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

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Genetic Approaches to Enhance Multiple Stress Tolerance in Maize

Genes ◽

10.3390/genes12111760 ◽

2021 ◽

Vol 12 (11) ◽

pp. 1760

Author(s):

Nenad Malenica ◽

Jasenka Antunović Dunić ◽

Lovro Vukadinović ◽

Vera Cesar ◽

Domagoj Šimić

Keyword(s):

Stress Tolerance ◽

Stress Responses ◽

Association Studies ◽

Metal Exposure ◽

Genome Wide Association Studies ◽

Haploid Induction ◽

Multiple Stress ◽

Resistant Varieties ◽

Maize Varieties ◽

Multiple Stress Tolerance

The multiple-stress effects on plant physiology and gene expression are being intensively studied lately, primarily in model plants such as Arabidopsis, where the effects of six stressors have simultaneously been documented. In maize, double and triple stress responses are obtaining more attention, such as simultaneous drought and heat or heavy metal exposure, or drought in combination with insect and fungal infestation. To keep up with these challenges, maize natural variation and genetic engineering are exploited. On one hand, quantitative trait loci (QTL) associated with multiple-stress tolerance are being identified by molecular breeding and genome-wide association studies (GWAS), which then could be utilized for future breeding programs of more resilient maize varieties. On the other hand, transgenic approaches in maize have already resulted in the creation of many commercial double or triple stress resistant varieties, predominantly weed-tolerant/insect-resistant and, additionally, also drought-resistant varieties. It is expected that first generation gene-editing techniques, as well as recently developed base and prime editing applications, in combination with the routine haploid induction in maize, will pave the way to pyramiding more stress tolerant alleles in elite lines/varieties on time.

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Genome-Wide Identification of CBL-CIPK Gene Family in Honeysuckle (Lonicera japonica Thunb.) and Their Regulated Expression Under Salt Stress

Frontiers in Genetics ◽

10.3389/fgene.2021.751040 ◽

2021 ◽

Vol 12 ◽

Author(s):

Luyao Huang ◽

Zhuangzhuang Li ◽

Qingxia Fu ◽

Conglian Liang ◽

Zhenhua Liu ◽

...

Keyword(s):

Salt Stress ◽

Protein Kinases ◽

Stress Responses ◽

Structure Prediction ◽

Functional Divergence ◽

Gene Families ◽

Plant Responses ◽

Interacting Protein ◽

Protein Motifs ◽

Insight Into

In plants, calcineurin B-like proteins (CBLs) are a unique group of Ca2+ sensors that decode Ca2+ signals by activating a family of plant-specific protein kinases known as CBL-interacting protein kinases (CIPKs). CBL-CIPK gene families and their interacting complexes are involved in regulating plant responses to various environmental stimuli. To gain insight into the functional divergence of CBL-CIPK genes in honeysuckle, a total of six LjCBL and 17 LjCIPK genes were identified. The phylogenetic analysis along with the gene structure analysis divided both CBL and CBL-interacting protein kinase genes into four subgroups and validated by the distribution of conserved protein motifs. The 3-D structure prediction of proteins shown that most LjCBLs shared the same Protein Data Bank hit 1uhnA and most LjCIPKs shared the 6c9Da. Analysis of cis-acting elements and gene ontology implied that both LjCBL and LjCIPK genes could be involved in hormone signal responsiveness and stress adaptation. Protein-protein interaction prediction suggested that LjCBL4 is hypothesized to interact with LjCIPK7/9/15/16 and SOS1/NHX1. Gene expression analysis in response to salinity stress revealed that LjCBL2/4, LjCIPK1/15/17 under all treatments gradually increased over time until peak expression at 72 h. These results demonstrated the conservation of salt overly sensitive pathway genes in honeysuckle and a model of Ca2+-LjCBL4/LjSOS3-LjCIPK16/LjSOS2 module-mediated salt stress signaling in honeysuckle is proposed. This study provides insight into the characteristics of the CBL-CIPK gene families involved in honeysuckle salt stress responses, which could serve as a foundation for gene transformation technology, to obtain highly salt-tolerant medicinal plants in the context of the global reduction of cultivated land.

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Genomic Analysis of Serratia plymuthica MBSA-MJ1: A Plant Growth Promoting Rhizobacteria That Improves Water Stress Tolerance in Greenhouse Ornamentals

Frontiers in Microbiology ◽

10.3389/fmicb.2021.653556 ◽

2021 ◽

Vol 12 ◽

Author(s):

Nathan P. Nordstedt ◽

Michelle L. Jones

Keyword(s):

Water Stress ◽

Plant Growth ◽

Stress Tolerance ◽

Stress Responses ◽

Plant Growth Promoting Rhizobacteria ◽

Serratia Plymuthica ◽

Water Stress Tolerance ◽

Plant Growth Promoting ◽

Growth Promoting

Water stress decreases the health and quality of horticulture crops by inhibiting photosynthesis, transpiration, and nutrient uptake. Application of plant growth promoting rhizobacteria (PGPR) can increase the growth, stress tolerance, and overall quality of field and greenhouse grown crops subjected to water stress. Here, we evaluated Serratia plymuthica MBSA-MJ1 for its ability to increase plant growth and quality of Petunia × hybrida (petunia), Impatiens walleriana (impatiens), and Viola × wittrockiana (pansy) plants recovering from severe water stress. Plants were treated weekly with inoculum of MBSA-MJ1, and plant growth and quality were evaluated 2 weeks after recovery from water stress. Application of S. plymuthica MBSA-MJ1 increased the visual quality and shoot biomass of petunia and impatiens and increased the flower number of petunia after recovery from water stress. In addition, in vitro characterizations showed that MBSA-MJ1 is a motile bacterium with moderate levels of antibiotic resistance that can withstand osmotic stress. Further, comprehensive genomic analyses identified genes putatively involved in bacterial osmotic and oxidative stress responses and the synthesis of osmoprotectants and vitamins that could potentially be involved in increasing plant water stress tolerance. This work provides a better understanding of potential mechanisms involved in beneficial plant-microbe interactions under abiotic stress using a novel S. plymuthica strain as a model.

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Genome-wide identification and characterization of GRAS transcription factors in tomato (Solanum lycopersicum)

PeerJ ◽

10.7717/peerj.3955 ◽

2017 ◽

Vol 5 ◽

pp. e3955 ◽

Cited By ~ 16

Author(s):

Yiling Niu ◽

Tingting Zhao ◽

Xiangyang Xu ◽

Jingfu Li

Keyword(s):

Gene Family ◽

Solanum Lycopersicum ◽

Stress Responses ◽

Expression Patterns ◽

Gene Families ◽

Shoot Meristem ◽

Axillary Shoot ◽

Multiple Sequence ◽

Genome Wide ◽

First Time

Solanum lycopersicum, belonging to Solanaceae, is one of the commonly used model plants. The GRAS genes are transcriptional regulators, which play a significant role in plant growth and development, and the functions of several GRAS genes have been recognized, such as, axillary shoot meristem formation, radial root patterning, phytohormones (gibberellins) signal transduction, light signaling, and abiotic/biotic stress; however, only a few of these were identified and functionally characterized. In this study, a gene family was analyzed comprehensively with respect to phylogeny, gene structure, chromosomal localization, and expression pattern; the 54 GRAS members were screened from tomato by bioinformatics for the first time. The GRAS genes among tomato, Arabidopsis, rice, and grapevine were rebuilt to form a phylogenomic tree, which was divided into ten groups according to the previous classification of Arabidopsis and rice. A multiple sequence alignment exhibited the typical GRAS domain and conserved motifs similar to other gene families. Both the segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in tomato; the expression patterns across a variety of tissues and biotic conditions revealed potentially different functions of GRAS genes in tomato development and stress responses. Altogether, this study provides valuable information and robust candidate genes for future functional analysis for improving the resistance of tomato growth.

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Distinct carbohydrate and lipid-based molecular patterns within lipopolysaccharides from Burkholderia cepacia contribute to defense-associated differential gene expression in Arabidopsis thaliana

Innate Immunity ◽

10.1177/1753425910392609 ◽

2011 ◽

Vol 18 (1) ◽

pp. 140-154 ◽

Cited By ~ 38

Author(s):

Ntakadzeni E Madala ◽

Antonio Molinaro ◽

Ian A Dubery

Keyword(s):

Arabidopsis Thaliana ◽

Protein Interactions ◽

Stress Responses ◽

Burkholderia Cepacia ◽

Lipid A ◽

Metabolic Reprogramming ◽

Basal Resistance ◽

Signal Perception ◽

Initial Perception ◽

Molecular Patterns

Lipopolysaccharides are structural components within the cell walls of Gram-negative bacteria. The LPSs as microbe-associated molecular pattern (MAMP) molecules can trigger defense-related responses involved in MAMP-triggered immunity and basal resistance in plants, presumably from an initial perception event. LPS from Burkholderia cepacia as well as two fragments, the glycolipid, lipid A and the polysaccharide (OPS-core) chain, were used to treat Arabidopsis thaliana seedlings to evaluate the eliciting activities of the individual LPS sub-domains by means of Annealing Control Primer-based Differential Display transcript profiling. Genes found to be up-regulated encode for proteins involved in signal perception and transduction, transcriptional regulation and defense – and stress responses. Furthermore, genes encoding proteins involved in chaperoning, secretion, protein–protein interactions and protein degradation were differentially expressed. It is concluded that intact LPS, as well as the two sub-components, induced the expression of a broad range of genes associated with perception and defense as well as metabolic reprogramming of cellular activities in support of immunity and basal resistance. Whilst the lipid A and OPS moieties were able to up-regulate sub-sets of defense-associated genes over the same spectrum of categories as intact LPS, the up-regulation observed with intact LPS was the more comprehensive, suggesting that the lipid A and glycan molecular patterns of the molecule act as partial agonists, but that the intact LPS structure is required for full agonist activity.

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Transgenic Rice Expressing Isoflavone Synthase Gene from Soybean Shows Resistance against Blast Fungus (Magnaporthe oryzae)

Plant Disease ◽

10.1094/pdis-08-20-1777-re ◽

2021 ◽

Author(s):

Suresh Pokhrel ◽

Sathish K Ponniah ◽

Yulin Jia ◽

Oliver Yu ◽

Muthusamy Manoharan

Keyword(s):

Disease Resistance ◽

Transgenic Rice ◽

Magnaporthe Oryzae ◽

Plant Disease Resistance ◽

Rice Blast ◽

Plant Disease ◽

Plant Secondary Metabolites ◽

Single Copy ◽

Transgenic Lines ◽

Isoflavone Synthase

The isoflavones are a group of plant secondary metabolites primarily synthesized in legumes and are known for their role in improving human health and plant disease resistance. The isoflavones, especially genistein, act as precursors for the production of phytoalexins, which may induce broad-spectrum disease resistance in plants. In the present study, we screened transgenic rice lines expressing the isoflavone synthase (GmIFS1) gene from soybean for rice blast (Magnaporthe oryzae) resistance. Two homozygous transgenic lines (I2 and I10), based on single copy gene integration, were identified. The expression of GmIFS1 in transgenic lines was confirmed by qRT-PCR. Genistein was detected in the transgenic lines using LC-MS/MS. Subsequently, the transgenic lines were evaluated against the rice blast pathogen, isolate YJ54 (race IB-54). The results indicated that more than 60% of the plants in both the lines (I2 and I10) showed resistance against the blast pathogen. The progenies of one of the resistant transgenic lines (I10) also showed more than 65% resistance against rice blast. The resistance of these transgenic lines against rice blast may be attributed to the synthesis of isoflavone (genistein) in rice.

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Expression of thaumatin, a new type of alternative sweetener in rice

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha48311676 ◽

2020 ◽

Vol 48 (3) ◽

pp. 1276-1291

Author(s):

Shahina AKTER ◽

Md. Amdadul HUQ ◽

Yu-Jin JUNG ◽

Kwon-Kyoo KANG

Keyword(s):

Transgenic Rice ◽

Oryza Sativa L ◽

Plasmid Vector ◽

Single Copy ◽

Cauliflower Mosaic Virus ◽

Pcr Analysis ◽

35S Promoter ◽

Alternative Sweetener ◽

Sweet Proteins ◽

Transgenic Lines

Sweet proteins are the natural alternative to the artificial sweeteners as well as flavor enhancers. Among other sweet protein, thaumatin protein was isolated from Thaumatococcus daniellii Benth plant fruit. In this study, pinII Ti plasmid vector was constructed with thaumatin gene, where thaumatin was placed under the control of the duel cauliflower mosaic virus 35S promoter into rice (Oryza sativa L. var. japonica cv. ‘Dongjinbyeo’) by Agrobacterium-mediated transformation to generate transgenic plants. Thirteen plant lines were regenerated and the transgenic rice lines were confirmed by different molecular analysis. The genomic PCR result revealed that all of the plant lines were transgenic. The single copy and intergenic plant lines were selected by Taqman PCR analysis and FST analysis, respectively. Expression of thaumatin gene in transgenic rice resulted in the accumulation of thaumatin protein in the leave. Thaumatin protein was also accumulated in leave of T1 generation. Sensory analysis result suggested that the thaumatin protein expressing transgenic lines exerted sweet tasting activity. These results demonstrated that thaumatin was expressed in transgenic rice plants.

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Humic acid enhances heat stress tolerance via transcriptional activation of Heat-Shock Proteins in Arabidopsis

Scientific Reports ◽

10.1038/s41598-020-71701-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Joon-Yung Cha ◽

Sang-Ho Kang ◽

Imdad Ali ◽

Sang Cheol Lee ◽

Myung Geun Ji ◽

...

Keyword(s):

Heat Stress ◽

Humic Acid ◽

Heat Shock ◽

Stress Tolerance ◽

Transcriptional Activation ◽

Molecular Mechanisms ◽

Agronomic Traits ◽

Enrichment Analysis ◽

Gene Families ◽

Heat Stress Tolerance

Abstract Humic acid (HA) is composed of a complex supramolecular association and is produced by humification of organic matters in soil environments. HA not only improves soil fertility, but also stimulates plant growth. Although numerous bioactivities of HA have been reported, the molecular evidences have not yet been elucidated. Here, we performed transcriptomic analysis to identify the HA-prompted molecular mechanisms in Arabidopsis. Gene ontology enrichment analysis revealed that HA up-regulates diverse genes involved in the response to stress, especially to heat. Heat stress causes dramatic induction in unique gene families such as Heat-Shock Protein (HSP) coding genes including HSP101, HSP81.1, HSP26.5, HSP23.6, and HSP17.6A. HSPs mainly function as molecular chaperones to protect against thermal denaturation of substrates and facilitate refolding of denatured substrates. Interestingly, wild-type plants grown in HA were heat-tolerant compared to those grown in the absence of HA, whereas Arabidopsis HSP101 null mutant (hot1) was insensitive to HA. We also validated that HA accelerates the transcriptional expression of HSPs. Overall, these results suggest that HSP101 is a molecular target of HA promoting heat-stress tolerance in Arabidopsis. Our transcriptome information contributes to understanding the acquired genetic and agronomic traits by HA conferring tolerance to environmental stresses in plants.

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