In silico characterisation and functional validation of chilling tolerant divergence 1 (COLD1) gene in monocots during abiotic stress

Coexpression Regulation of New and Ancient Genes in the Dynamic Transcriptome Landscape of Stem and Rhizome Development in "Bainianzhe"-An Ancient Chinese Sugarcane Variety Ratooned for Nearly 300 Years

The sucrose yield in sugarcane largely depends on stem morphology, including length, diameter and sugar content, making sugarcane stem a key trait in breeding. The "Bainianzhe" variety from Songxi County, Fujian Province, possesses both aerial stems and rhizomes, providing a unique model for studying stem development. We performed a spatiotemporal transcriptomic analysis of the base, middle and apical sections of both aerial stems and rhizomes. The analysis categorized transcriptomes by developmental stage-base, middle and apical-rather than environmental differences. Apical segments were enriched with genes related to cell proliferation, while base segments were linked to senescence and fibrosis. Gene regulatory networks revealed key TFs involved in stem development. Orphan genes may be involved in rhizome development through coexpression networks. Plant hormones, especially genes involved in ABA and GAs synthesis, were highly expressed in rhizomes. Thiamine-related genes were also more prevalent in rhizomes. Furthermore, the apical segments of rhizomes enriched in photosynthesis-related genes suggest adaptations to light exposure. Low average temperatures in Songxi have led to unique cold acclimation in Bainianzhe, with rhizomes showing higher expression of genes linked to unsaturated fatty acid synthesis and cold-responsive calcium signalling. This indicates that rhizomes may have enhanced cold tolerance, aiding in the plant's overwintering success.

Transgenic sugarcane overexpressing Glyoxalase III improved germination and biomass production at formative stage under salinity and water-deficit stress conditions

The glyoxalase system, involving Glyoxalase I (GlyI) and Glyoxalase II (Gly II), plays a vital role in abiotic stress tolerance in plants. A novel enzyme Glyoxalase III (Gly III) was found recently from bacteria, yeast, and plant species. This enzyme provides a new way to detoxify Methylglyoxal (MG), a cytotoxic α-oxoaldehyde, which, in excess, can cause complete cell destruction by forming Reactive Oxygen Species (ROS) and Advanced Glycation End products (AGEs) or DNA/RNA mutation. In this background, the current study examined sugarcane transgenic events that exhibit an increase in expression of EaGly III, to assess their performance in terms of germination and biomass production during formative stage under stress conditions. Southern blot analysis outcomes confirmed the integration of transgene in the transgenic plants. The results from quantitative RT-PCR analyses confirmed high expression levels of EaGly III in transgenic events compared to wild type (WT) under salinity (100 and 200 mM NaCl) and drought (withholding watering) conditions. Transgenic events exhibited enhanced biomass productivity ranged between 0.141 Kg/pot and 0.395 Kg/pot under 200 mM salinity and 0.262 Kg/pot and 0.666 Kg/pot under drought stress. Further, transgenic events observed significantly higher germination rates under salinity and drought conditions compared to that of WT. Subcellular localization prediction by EaGlyIII-GFP fusion expression in sugarcane callus showed that it is distributed across the cytoplasm, thus indicating its widespread activity within the cell. These results strongly suggest that enhancing EaGly III activity is a useful strategy to improve the salinity and drought-tolerance in sugarcane as well as other crops.

Evaluation of Novel HLM Peptide Activity and Toxicity against Planktonic and Biofilm Bacteria: Comparison to Standard Antibiotics

BACKGROUND

Antibiotic resistance is one of the main concerns of public health, and the whole world is trying to overcome such a challenge by finding novel therapeutic modalities and approaches. This study has applied the sequence hybridization approach to the original sequence of two cathelicidin natural parent peptides (BMAP-28 and LL-37) to design a novel HLM peptide with broad antimicrobial activity.

METHODS

The physicochemical characteristics of the newly designed peptide were determined. As well, the new peptide's antimicrobial activity (Minimum Inhibitory Concentration (MIC), Minimum Bacterial Eradication Concentration (MBEC), and antibiofilm activity) was tested on two control (Staphylococcus aureus ATCC 29213, Escherichia coli ATCC 25922) and two resistant (Methicillin-resistant Staphylococcus aureus (MRSA) ATCC BAA41, New Delhi metallo-beta- lactamase-1 Escherichia coli ATCC BAA-2452) bacterial strains. Furthermore, synergistic studies have been applied to HLM-hybridized peptides with five conventional antibiotics by checkerboard assays. Also, the toxicity of HLM-hybridized peptide was studied on Vero cell lines to obtain the IC50 value. Besides the percentage of hemolysis action, the peptide was tested in freshly heparinized blood.

RESULTS

The MIC values for the HLM peptide were obtained as 20, 10, 20, and 20 μM, respectively. Also, the results showed no hemolysis action, with low to slightly moderate toxicity action against mammalian cells, with an IC50 value of 10.06. The Biomatik corporate labs, where HLM was manufactured, determined the stability results of the product by Mass Spectrophotometry (MS) and High-performance Liquid Chromatography (HPLC) methods. The HLM-hybridized peptide exhibited a range of synergistic to additive antimicrobial activities upon combination with five commercially available different antibiotics. It has demonstrated the biofilm-killing effects in the same concentration required to eradicate the control strains.

CONCLUSION

The results indicated that HLM-hybridized peptide displayed a broad-spectrum activity toward different bacterial strains in planktonic and biofilm forms. It showed synergistic or additive antimicrobial activity upon combining with commercially available different antibiotics.

Growing Conditions and Varietal Ecologies Differently Regulates the Growth-regulating-factor (GRFs) Gene Family in Rice

Background

Growth-regulating factors (GRFs) are crucial in rice for controlling plant growth and development. Among the rice cultivation practices, aerobic methods are water efficient but result in significant yield reduction relative to non-aerobic cultivation. Therefore, mechanistic insights into aerobic rice cultivation are important for improving the aerobic performance of rice.

Objectives

This study aimed to examine the evolution of GRFs in different rice species, analyse the phenotypic differences between aerobic and non-aerobic conditions in three rice varieties, and assess the expression of GRFs in these varieties under both aerobic and non-aerobic conditions.

Materials and Methods

This study comprehensively examined the GRFs gene family in 11 rice species (Oryza barthii, Oryza brachyantha, Oryza glaberrima, Oryza glumipatula, Oryza sativa subsp. indica, Oryza longistaminata, Oryza meridionalis, Oryza nivara, Oryza punctata, Oryza rufipogon, Oryza sativa subsp. japonica) focusing on phylogenetic analysis. Additionally, the expression patterns of 12 GRFs were investigated in three distinct genotypes of O. sativa subsp. indica rice, under both non-aerobic and aerobic conditions.

Results

Three major phylogenetic clades were formed based on conserved motifs in the 123 GRFs proteins in eleven rice species. Further, novel motifs were identified especially in O. longistaminata indicative of the species level evolutionary differences in rice. Among the trait performance, the number of tillers was reduced by ~ 36% under aerobic conditions, but the reduction was found to be less in CR Dhan 201, an aerobic variety. Besides, three GRFs namely GRF3, GRF4, and GRF7 were found to be distinct in expression between aerobic and non-aerobic conditions.

Conclusion

Three GRF genes namely GRF3, GRF4, and GRF7 could be associated with the aerobic adaptation in rice.

Coordination of m6A mRNA Methylation and Gene Transcriptome in Sugarcane Response to Drought Stress

The N6-methyladenosine (m6A) methylation of mRNA is involved in biological processes essential for plant growth. To explore the m6A modification of sugarcane and reveal its regulatory function, methylated RNA immunoprecipitation sequencing (MeRIP-seq) was used to construct the m6A map of sugarcane. In this study, m6A sites of sugarcane transcriptome were significantly enriched around the stop codon and within 3'-untranslated regions (3'UTR). Gene ontology (GO) analysis showed that the m6A modification genes are associated with metabolic biosynthesis. In addition, the m6A modification of drought-resistant transcript mRNA increased significantly under drought (DR) treatment, resulting in enhanced mRNA stability, which is involved in regulating sugarcane drought resistance. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results showed that differentially methylated peak (DMP) modification of differentially expressed genes (DEGs) in DR were particularly associated with abscisic acid (ABA) biosynthesis. The upregulated genes were significantly enriched in the ABA metabolism, ethylene response, fatty acid metabolism, and negative regulation of the abscisic acid activation signaling pathway. These findings provide a basis and resource for sugarcane RNA epigenetic studies and further increase our knowledge of the functions of m6A modifications in RNA under abiotic stress.

Isolation of 5' regulatory region of COLD1 gene and its functional characterization through transient expression analysis in tobacco and sugarcane

Chilling Tolerant Divergence 1 (COLD1) gene consists of Golgi pH Receptor (GPHR) as well as Abscisic Acid-linked G Protein-Coupled Receptor (ABA_GPCR), which are the major transmembrane proteins in plants. This gene expression has been found to be differentially regulated, under various stress conditions, in wild Saccharum-related genera, Erianthus arundinaceus, compared to commercial sugarcane variety. In this study, Rapid Amplification of Genomic Ends (RAGE) technique was employed to isolate the 5' upstream region of COLD1 gene to gain knowledge about the underlying stress regulatory mechanism. The current study established the cis-acting elements, main promoter regions, and Transcriptional Start Site (TSS) present within the isolated 5' upstream region (Cold1P) of COLD1, with the help of specific bioinformatics techniques. Phylogenetic analysis results revealed that the isolated Cold1P promoter is closely related to the species, Sorghum bicolor. Cold1P promoter-GUS gene construct was generated in pCAMBIA 1305.1 vector that displayed a constitutive expression of the GUS reporter gene in both monocot as well as dicot plants. The histochemical GUS assay outcomes confirmed that Cold1P can drive expression in both monocot as well as dicot plants. Cold1P's activities under several abiotic stresses such as cold, heat, salt, and drought, revealed its differential expression profile in commercial sugarcane variety. The highest activity of the GUS gene was found after 24 h of cold stress, driven by the isolated Cold1P promoter. The outcomes from GUS fluorimetric assay correlated with that of the GUS expression findings. This is the first report on Cold1P isolated from the species, E. arundinaceus.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03650-8.

Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

Erianthus arundinaceus [Retzius] Jeswiet, a wild relative of sugarcane has a high biomass production potential and a reservoir of many genes for superior agronomic traits and tolerance to biotic and abiotic stresses. A comparative physiological, anatomical and root transcriptome analysis were carried out to identify the salt-responsive genes and metabolic pathways associated with salt-tolerant E. arundinaceus genotype IND99-907 and salinity-sensitive sugarcane genotype Co 97010. IND99-907 recorded growth of young leaves, higher proline content, higher relative water content, intact root anatomical structures and lower Na+/K+, Ca2+/K+ and Mg2+/K+ ratio as compared to the sugarcane genotype Co 97010. We have generated four de novo transcriptome assemblies between stressed and control root samples of IND99-907 and Co 97010. A total of 649 and 501 differentially expressed genes (FDR<0.01) were identified from the stressed and control libraries of IND99-907 and Co 97010 respectively. Genes and pathways related to early stress-responsive signal transduction, hormone signalling, cytoskeleton organization, cellular membrane stabilization, plasma membrane-bound calcium and proton transport, sodium extrusion, secondary metabolite biosynthesis, cellular transporters related to plasma membrane-bound trafficking, nucleobase transporter, clathrin-mediated endocytosis were highly enriched in IND99-907. Whereas in Co 97010, genes related to late stress-responsive signal transduction, electron transport system, senescence, protein degradation and programmed cell death, transport-related genes associated with cellular respiration and mitochondrial respiratory chain, vesicular trafficking, nitrate transporter and fewer secondary metabolite biosynthetic genes were highly enriched. A total of 27 pathways, 24 biological processes, three molecular functions and one cellular component were significantly enriched (FDR≤ 0.05) in IND99-907 as compared to 20 pathways, two biological processes without any significant molecular function and cellular components in Co 97010, indicates the unique and distinct expression pattern of genes and metabolic pathways in both genotypes. The genomic resources developed from this study is useful for sugarcane crop improvement through development of genic SSR markers and genetic engineering approaches.

Ectopic expression of DJ-1/PfpI domain containing Erianthus arundinaceus Glyoxalase III (EaGly III) enhances drought tolerance in sugarcane

Sugarcane transgenic overexpressing EaGly III from Erianthus arundinaceus showed enhanced water deficit stress tolerance. Methylglyoxal (MG), an α-ketoaldehyde formed from either glycolysis or TCA cycle, is capable of causing total cellular damage via the generation of reactive oxygen species (ROS), advanced glycation end products (AGEs) and nucleic acid degradation. Glyoxalase pathway is a ubiquitous pathway known for detoxification of MG, involving key enzymes glyoxalase I (Gly I) and glyoxalase II (Gly II). Recently, a novel and an additional enzyme in glyoxalase pathway, viz., glyoxalase III (Gly III), has been discovered which possesses DJ-1/PfpI domain recognized for detoxifying MG in a single step process without requirement of any coenzyme. In the present study, a Gly III gene isolated from Erianthus arundinaceus, a wild relative of sugarcane, overexpressed in commercially cultivated sugarcane hybrid Co 86032 was assessed for drought tolerance. Morphometric observations revealed that transgenic sugarcane overexpressing EaGly III acquired drought tolerance trait. Oxidative damage caused by triggering generation of ROS has been determined to be low in transgenic plants as compared to wild type (WT). Transgenics resulted in higher relative water content, chlorophyll content, gas exchange parameters, photosynthetic efficiency, proline content and soluble sugars upon water deficit stress. In addition, higher and stable level of superoxide dismutase and peroxidase activities were observed along with minimal lipid peroxidation during drought stress signifying the tolerance mechanism exhibited by transgenic events. There was no significant structural change observed in the root anatomy of transgenic plants. Altogether, EaGly III gene could be considered as a potential candidate for conferring water deficit stress tolerance for sugarcane and other agricultural crops.

Isolation, characterization and expression analysis of stress responsive plant nuclear transcriptional factor subunit (NF-YB2) from commercial Saccharum hybrid and wild relative Erianthus arundinaceus

Plant nuclear factor (NF-Y) is a transcription activating factor, consisting of three subunits, and plays a key regulatory role in many stress-responsive mechanisms including drought and salinity stresses. NF-Ys function both as complex and individual subunits. Considering the importance of sugarcane as a commercial crop with high socio-economic importance and the crop being affected mostly by water deficit stress and salinity stress causing significant yield loss, nuclear transcriptional factor NF-YB2 was focused in this study. Plant nuclear factor subunit B2 from Erianthus arundinaceus (EaNF-YB2), a wild relative of sugarcane which is known for its drought and salinity stress tolerance, and commercial Saccharum hybrid Co 86032 (ShNF-YB2) was isolated and characterized. Both EaNF-YB2 and ShNF-YB2 genes are 543 bp long that encodes for a polypeptide of 180 amino acid residues. Comparison of EaNF-YB2 and ShNF-YB2 gene sequences revealed nucleotide substitutions at nine positions corresponding to three synonymous and six nonsynonymous amino acid substitutions that resulted in variations in physiochemical properties. However, multiple sequence alignment (MSA) of NF-YB2 proteins showed conservation of functionally important amino acid residues. In silico analysis revealed NF-YB2 to be a hydrophilic and intracellular protein, and EaNF-YB2 is thermally more stable than that of ShNF-YB2. Phylogenetic analysis suggested the lower rate of evolution of NF-YB2. Subcellular localization in sugarcane callus revealed NF-YB2 localization at nucleus that further evidenced it to be a transcription activation factor. Comparative RT-qPCR experiments showed a significantly higher level of NF-YB2 expression in E. arundinaceus when compared to that in the commercial Saccharum hybrid Co 86032 under drought and salinity stresses. Hence, EaNF-YB2 could be an ideal candidate gene, and its overexpression in sugarcane through genetic engineering approach might enhance tolerance to drought and salinity stresses.

Identification of novel OsCML16 target proteins and differential expression analysis under abiotic stresses in rice

Calmodulin-like proteins (CMLs) have been shown to play key regulatory roles in calcium signaling in plants. However, few bona-fide CMLs binding proteins have been characterized in rice, a monocot model plant. Here, through large-scale screening of a yeast-two hybrid (Y2H) cDNA library with OsCML16 as a bait, six new putative interacting partners of OsCML16 were discovered and confirmed by both pairwise Y2H and bimolecular fluorescence complementation (BiFC) assays. Interestingly, the in vitro peptide-binding assays manifested that OsERD2 could bind both OsCaM1 and OsCML16 whereas other five target proteins could specifically bind OsCML16 but not OsCaM1. Furthermore, Ca²⁺ and TFP, a calmodulin (CaM) antagonist, were involved in the ABA-induced transcription of OsCML16 and its target genes, and they were also obviously induced by cold, drought, and salt stresses. Taken together, our new findings have provided the basis for the novel signaling pathways of OsCML16 in the abiotic stress response in rice.