MusaMPK5, a mitogen activated protein kinase is involved in regulation of cold tolerance in banana

Discovery of gene regulation mechanisms associated with uniconazole-induced cold tolerance in banana using integrated transcriptome and metabolome analysis

BACKGROUND

The gibberellic acid (GA) inhibitor, uniconazole, is a plant growth regulator commonly used in banana cultivation to promote dwarfing but also enhances the cold resistance in plants. However, the mechanism of this induced cold resistance remains unclear.

RESULTS

We confirmed that uniconazole induced cold tolerance in bananas and that the activities of Superoxide dismutase and Peroxidase were increased in the uniconazole-treated bananas under cold stress when compared with the control groups. The transcriptome and metabolome of bananas treated with or without uniconazole were analyzed at different time points under cold stress. Compared to the control group, differentially expressed genes (DEGs) between adjacent time points in each uniconazole-treated group were enriched in plant-pathogen interactions, MAPK signaling pathway, and plant hormone signal transduction, which were closely related to stimulus-functional responses. Furthermore, the differentially abundant metabolites (DAMs) between adjacent time points were enriched in flavone and flavonol biosynthesis and linoleic acid metabolism pathways in the uniconazole-treated group than those in the control group. Temporal analysis of DEGs and DAMs in uniconazole-treated and control groups during cold stress showed that the different expression patterns in the two groups were enriched in the linoleic acid metabolism pathway. In addition to strengthening the antioxidant system and complex hormonal changes caused by GA inhibition, an enhanced linoleic acid metabolism can protect cell membrane stability, which may also be an important part of the cold resistance mechanism of uniconazole treatment in banana plants.

CONCLUSIONS

This study provides information for understanding the mechanisms underlying inducible cold resistance in banana, which will benefit the production of this economically important crop.

Genome-Wide Identification of the MAPK and MAPKK Gene Families in Response to Cold Stress in Prunus mume

Protein kinases of the MAPK cascade family (MAPKKK-MAPKK-MAPK) play an essential role in plant stress response and hormone signal transduction. However, their role in the cold hardiness of Prunus mume (Mei), a class of ornamental woody plant, remains unclear. In this study, we use bioinformatic approaches to assess and analyze two related protein kinase families, namely, MAP kinases (MPKs) and MAPK kinases (MKKs), in wild P. mume and its variety P. mume var. tortuosa. We identify 11 PmMPK and 7 PmMKK genes in the former species and 12 PmvMPK and 7 PmvMKK genes in the latter species, and we investigate whether and how these gene families contribute to cold stress responses. Members of the MPK and MKK gene families located on seven and four chromosomes of both species are free of tandem duplication. Four, three, and one segment duplication events are exhibited in PmMPK, PmvMPK, and PmMKK, respectively, suggesting that segment duplications play an essential role in the expansion and evolution of P. mume and its gene variety. Moreover, synteny analysis suggests that most MPK and MKK genes have similar origins and involved similar evolutionary processes in P. mume and its variety. A cis-acting regulatory element analysis shows that MPK and MKK genes may function in P. mume and its variety's development, modulating processes such as light response, anaerobic induction, and abscisic acid response as well as responses to a variety of stresses, such as low temperature and drought. Most PmMPKs and PmMKKs exhibited tissue-specifific expression patterns, as well as time-specific expression patterns that protect them through cold. In a low-temperature treatment experiment with the cold-tolerant cultivar P. mume 'Songchun' and the cold-sensitive cultivar 'Lve', we find that almost all PmMPK and PmMKK genes, especially PmMPK3/5/6/20 and PmMKK2/3/6, dramatically respond to cold stress as treatment duration increases. This study introduces the possibility that these family members contribute to P. mume's cold stress response. Further investigation is warranted to understand the mechanistic functions of MAPK and MAPKK proteins in P. mume development and response to cold stress.

OsLPXC negatively regulates tolerance to cold stress via modulating oxidative stress, antioxidant defense and JA accumulation in rice

Exposure of crops to low temperature (LT) during emerging and reproductive stages influences their growth and development. In this study, we have isolated a cold induced, nucleus-localized lipid A gene from rice named OsLPXC, which encodes a protein of 321 amino acids. Knockout of OsLPXC resulted in enhance sensitivity to LT stress in rice, with increased accumulation of reactive oxygen species (ROS), malondialdehyde and electrolyte leakage, while expression and activities of antioxidant enzymes were significantly suppressed. The accumulation of chlorophyll content and net photosynthetic rate of knockout plants were also decreased compared with WT under LT stress. The functional analysis of differentially expressed genes (DEGs), showed that numerous genes associated with antioxidant defense, photosynthesis, cold signaling were solely expressed and downregulated in oslpxc plants compared with WT under LT. The accumulation of methyl jasmonate (MeJA) in leave and several DEGs related to the jasmonate biosynthesis pathway were significantly downregulated in OsLPXC knockout plants, which showed differential levels of MeJA regulation in WT and knockout plants in response to cold stress. These results indicated that OsLPXC positively regulates cold tolerance in rice via stabilizing the expression and activities of ROS scavenging enzymes, photosynthetic apparatus, cold signaling genes, and jasmonate biosynthesis.

Functional characterization of 5'-regulatory region of flavonoid 3',5'-hydroxylase-1 gene of banana plants

Generation of crops with broad-spectrum tolerance to biotic and abiotic stress conditions depends upon availability of genetic elements suitable for varied situations and diverse genotypes. Here, we characterize the 5'-upstream regulatory region of flavonoid 3'5'-hydroxylase-1 (F3'5'H-1) gene from banana and analyzed its tissue-specific and stress-mediated activation in genetic background of tobacco plants. MusaF3'5'H-1 is a stress-responsive gene as its expression is induced in banana after application of salicylic acid and methyl jasmonate while its transcript levels were drastically reduced in response to drought, high salinity and abscisic acid. P_MusaF3'5'H-1 harbours cis-elements associated with stress conditions and those responsible for tissue-specific expression. Transgenic lines harbouring P_MusaF3'5'H-1-GUS displays strong GUS expression in guard cells of stomata indicating guard cell preferred activity of P_MusaF3'5'H-1 while its activity was undetectable in roots. Drought and high salinity induce strong expression of GUS in transgenic tobacco lines and exposure to abscisic acid, salicylic acid and methyl jasmonate revealed distinct profiles of GUS expression in transgenic lines confirming involvement of F3'5'H-1 in plant stress responses. Fluorescent β-galactosidase assay revealed induction profiles of P_MusaF3'5'H-1 at different time points in transgenic lines exposed to salicylic acid and abscisic acid while strong suppression in GUS expression was observed after application of methyl jasmonate. The guard cell preferred activity of P_MusaF3'5'H-1 and stress-mediated expression profiles of MusaF3'5'H-1 indicated the suitability of P_MusaF3'5'H-1 for generating stress-enduring crops and analyzing guard cell functions.

MusaNAC29-like transcription factor improves stress tolerance through modulation of phytohormone content and expression of stress responsive genes

Understanding the molecular mechanisms governed by genes and cross-talks among stress signaling pathways is vital for generating a broad view on stress responses in plants. Here, we analysed the effects of MusaNAC29-like transcription factor of banana on stress responses and report the quantitative modulation of phytohormone and flavonoid content and analysed the growth parameters and yield trait in transgenic banana plants. Expression of MusaNAC29-like transcription factor was strongly altered in responses to stress conditions and application of signaling molecules. Under control conditions, P_{MusaNAC29-like}-GUS is activated in cells bordering xylem vessel elements and is strongly triggered in other cells types after influence of salicylic acid and abscisic acid. Transgenic banana plants of cultivar Rasthali and Grand Naine overexpressing MusaNAC29-like transcription factor displayed superior tolerance towards drought and salinity stress. LC-MS analysis indicated elevated levels of jasmonic acid and salicylic acid while content of zeatin was significantly reduced in leaves of transgenic banana lines. Transgenic banana lines displayed increased levels of gallic acid, coumaric acid, naringenin, chlorogenic acid while levels of vanillic acid and piperine were significantly reduced. Expression of stress related genes coding for antioxidants, thiol peptidase proteins, cold-regulated proteins, late embryogenesis abundant proteins, ethylene-responsive transcription factors, bHLH proteins, jasmonate-zim-domain proteins and WRKY transcription factors were significantly induced in transgenic banana lines. Though MusaNAC29-like transcription factor improved stress tolerance, its overexpression resulted in retarded growth of transgenic lines resulting in reduced yield of banana fruits.

Genome-Wide Association Mapping Identifies New Candidate Genes for Cold Stress and Chilling Acclimation at Seedling Stage in Rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a chilling-sensitive staple food crop, and thus, low temperature significantly affects rice growth and yield. Many studies have focused on the cold shock of rice although chilling acclimation is more likely to happen in the field. In this paper, a genome-wide association study (GWAS) was used to identify the genes that participated in cold stress and chilling accumulation. A total of 235 significantly associated single-nucleotide polymorphisms (SNPs) were identified. Among them, we detected 120 and 88 SNPs for the relative shoot fresh weight under cold stress and chilling acclimation, respectively. Furthermore, 11 and 12 quantitative trait loci (QTLs) were identified for cold stress and chilling acclimation, respectively, by integrating the co-localized SNPs. Interestingly, we identified 10 and 15 candidate genes in 11 and 12 QTLs involved in cold stress and chilling acclimation, respectively, and two new candidate genes (LOC_Os01g62410, LOC_Os12g24490) were obviously up-regulated under chilling acclimation. Furthermore, OsMYB3R-2 (LOC_Os01g62410) that encodes a R1R2R3 MYB gene was associated with cold tolerance, while a new C3HC4-type zinc finger protein-encoding gene LOC_Os12g24490 was found to function as a putative E3 ubiquitin-protein ligase in rice. Moreover, haplotype, distribution, and Wright’s fixation index (FST) of both genes showed that haplotype 3 of LOC_Os12g24490 is more stable in chilling acclimation, and the SNP (A > T) showed a difference in latitudinal distribution. FST analysis of SNPs in OsMYB3R-2 (LOC_Os01g62410) and LOC_Os12g24490 indicated that several SNPs were under selection in rice indica and japonica subspecies. This study provided new candidate genes in genetic improvement of chilling acclimation response in rice.

Infection by Pseudocercospora musae leads to an early reprogramming of the Musa paradisiaca defense transcriptome

Deep sequencing technologies such as RNA sequencing can help unravel mechanisms governing defense or resistance responses in plant-pathogen interactions. Several studies have been carried out to investigate the transcriptomic changes in Musa germplasm against Yellow Sigatoka disease, but the defense response of Musa paradisiaca has not been investigated so far. We carried out transcriptome sequencing of M. paradisiaca var. Kachkal infected with the pathogen Pseudocercospora musae and found that a vast set of genes were upregulated while many genes were downregulated in the resistant cultivar as a result of infection. After transcriptome assembly and differential gene expression analysis, 429 upregulated and 156 downregulated genes were filtered out (considering fold change ± 2, p < 0.01). Functional annotation of the differentially expressed genes (DEGs) enriched the upregulated genes into 49 gene ontology (GO) classes of biological processes (BP), 20 classes of molecular function (MF) and 9 classes of cellular component (CC). Similarly, the downregulated genes were classified into 35 GO classes of BP, 28 classes of MF and 6 classes of CC. The KEGG enrichment analysis revealed that the upregulated genes were most highly represented in 'metabolic' and 'biosynthesis of secondary metabolites' pathways. Additionally, 'plant hormone signal transduction', 'plant-pathogen interaction' and 'phenylpropanoid biosynthesis' pathways were also significantly enriched indicating their involvement in resistance responses against the pathogen. The RNA-seq analysis also depicts that a range of important defense-related genes are modulated as a result of infection, all of which are responsible for either mediating or activating resistance responses in the host. We studied and validated the expression profiles of ten important defense-related genes potentially involved in conferring resistance to the pathogen through qRT-PCR. Almost all the selected defense-related genes were found to be highly and significantly upregulated within 24 h post inoculation (hpi) and for some genes, the expression remained consistently high till the later time point of 72 hpi. These results, thus, indicate that the infection by P. musae leads to a rapid reprogramming of the defense transcriptome of the resistant banana cultivar. The defense-related genes identified to be modulated in response to infection are important not only for pathogen recognition and perception but also for activation and persistence of defense in the host.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03245-9.

Characterization of the early gene expression profile in Populus ussuriensis under cold stress using PacBio SMRT sequencing integrated with RNA-seq reads

Populus ussuriensis is an important and fast-growing afforestation plant species in north-eastern China. The whole-genome sequencing of P. ussuriensis has not been completed. Also, the transcriptional network of P. ussuriensis response to cold stress remains unknown. To unravel the early response of P. ussuriensis to chilling (3 °C) stress and freezing (-3 °C) stresses at the transcriptional level, we performed single-molecule real-time (SMRT) and Illumina RNA sequencing for P. ussuriensis. The SMRT long-read isoform sequencing led to the identification of 29,243,277 subreads and 575,481 circular consensus sequencing reads. Approximately 50,910 high-quality isoforms were generated, and 2272 simple sequence repeats and 8086 long non-coding RNAs were identified. The Ca2+ content and abscisic acid (ABA) content in P. ussuriensis were significantly increased under cold stresses, while the value in the freezing stress treatment group was significantly higher than the chilling stress treatment group. A total of 49 genes that are involved in the signal transduction pathways related to perception and transmission of cold stress signals, such as the Ca2+ signaling pathway, ABA signaling pathway and MAPK signaling cascade, were found to be differentially expressed. In addition, 158 transcription factors from 21 different families, such as MYB, WRKY and AP2/ERF, were differentially expressed during chilling and freezing treatments. Moreover, the measurement of physiological indicators and bioinformatics observations demonstrated the altered expression pattern of genes involved in reactive oxygen species balance and the sugar metabolism pathway during chilling and freezing stresses. This is the first report of the early responses of P. ussuriensis to cold stress, which lays the foundation for future studies on the regulatory mechanisms in cold-stress response. In addition the full-length reference transcriptome of P. ussuriensis deciphered could be used in future studies on P. ussuriensis.

Mitogen-Activated Protein Kinase and Substrate Identification in Plant Growth and Development

Mitogen-activated protein kinases (MAPKs) form tightly controlled signaling cascades that play essential roles in plant growth, development, and defense response. However, the molecular mechanisms underlying MAPK cascades are still very elusive, largely because of our poor understanding of how they relay the signals. The MAPK cascade is composed of MAPK, MAPKK, and MAPKKK. They transfer signals through the phosphorylation of MAPKKK, MAPKK, and MAPK in turn. MAPKs are organized into a complex network for efficient transmission of specific stimuli. This review summarizes the research progress in recent years on the classification and functions of MAPK cascades under various conditions in plants, especially the research status and general methods available for identifying MAPK substrates, and provides suggestions for future research directions.

The 5'-upstream region of WRKY18 transcription factor from banana is a stress-inducible promoter with strong expression in guard cells

Increasing crop productivity in an ever-changing environmental scenario is a major challenge for maintaining the food supply worldwide. Generation of crops having broad-spectrum pathogen resistance with the ability to cope with water scarcity is the only solution to feed the expanding world population. Stomatal closure has implications on pathogen colonization and drought tolerance. Recent studies have provided novel insights into networks involved in stomatal closure which is being used in biotechnological applications for improving crop endurance. Despite that genetic engineering of stomata requires guard cell preferred or specific regulatory regions to avoid undesirable side effects. In the present study, we describe the 5'-upstream regulatory region of the WRKY18 transcription factor of banana and functionally analyzed its stress meditated activation and strong guard cell preferred activity. Expression of MusaWRKY18 is augmented in leaves of banana cultivars Karibale Monthan, Rasthali and Grand Nain under multiple stress conditions suggesting its role in stress responses of banana plants. Transgenic tobacco lines harboring P_MusaWRKY18 -β-D-glucuronidase (GUS) were regenerated and GUS staining demonstrated substantial GUS expression in guard cells which corroborates with multiple Dof1 binding cis-elements in P_MusaWRKY18 . Fluorescent β-galactosidase assay demonstrated the stress-mediated strong induction profiles of P_MusaWRKY18 at different time points in transgenic tobacco lines exposed to drought, high-salinity, cold, and applications of abscisic acid, salicylic acid, methyl jasmonate, and ethephon. This study sheds novel insights into guard cell preferred expression of WRKY genes under stress and confirm the utility of P_MusaWRKY18 for exploring guard cell functions and guard cell engineering.

Studies on the tissue specific nature and stress inducible activation of the CHI-1 gene from banana

In the present study, the 5'-regulatory region of chalcone isomerase gene (MusaCHI-1) of banana was functionally analysed for its tissue specific, stress mediated and strong guard cell preferred activity. Expression of MusaCHI-1 was altered in leaves of banana plants exposed to various stress conditions and signalling molecules. Transgenic lines of tobacco harbouring P_MusaCHI-1-GUS displays prominent GUS staining in vascular region and guard cells of leaves which corroborates with array of Dof1 binding cis-elements in P_MusaCHI-1 region. Multiple cis-elements associated with various stress conditions were detected in P_MusaCHI-1 which directly correlates with alteration of MusaCHI-1 transcript level in banana exposed to stress conditions. GUS staining of transgenic tobacco plants harbouring P_MusaCHI-1-GUS and exposed to drought, salinity, and applications of methyl jasmonate and abscisic acid indicated activation of P_MusaCHI-1 under these conditions while exposure of salicylic acid strongly suppresses GUS expression from P_MusaCHI-1.

Cold stress in maize (Zea mays) is alleviated by the over-expression of Phytoglobin 1 (ZmPgb1.1)

Maize (Zea mays) plants over-expressing or suppressing the class 1 Phytoglobin (ZmPgb1.1) were evaluated for their ability to cope with low temperature stress. Cold treatment (10 °C day/4 °C night) depressed several gas exchange parameters including photosynthetic rate, stomatal conductance and transpiration, while elevated the levels of reactive oxygen species (ROS) and ROS-induced damage. These effects were attenuated by the over-expression of ZmPgb1.1, and aggravated when the level of the same gene was suppressed. Combination of transcriptomic and pharmacological studies revealed that over-expression of ZmPgb1.1 suppressed the level of nitric oxide (NO), which lowers the transcription of several Brassinosteroid (BR) biosynthetic and response genes. Cellular BR was required to induce the expression of ZmMPK5, a component of the mitogen-activated protein kinase (MAPK) cascade, which is known to be involved in the regulation of ROS-producing pathways. Experimental reduction of NO content, suppression of BR or inhibition of ZmMPK5 reverted the beneficial effects of ZmPgb1.1 over-expression, and increased plant susceptibility to cold stress through accumulation of ROS. Conversely, tolerance to cold was augmented in the ZmPgb1.1 down-regulating line when the levels of NO or BR were elevated. Together, this study demonstrates a novel role of ZmPgb1.1 in modulating plant performance to cold stress, and integrates the ZmPgb1.1 response in a model requiring NO and BR to alleviate oxidative stress through ZmMPK5.

Molecular cloning and sequence analysis of a mitogen-activated protein kinase gene in the Antarctic yeast Rhodotorula mucilaginosa AN5

BACKGROUND

The mitogen-activated protein kinase (MAPK) cascades play important roles in various signaling transduction networks of biotic and abiotic stress responses. However, MAPK signaling pathways in cold-active yeast Rhodotorula mucilaginosa have not been reported comprehensively.

METHODS AND RESULTS

In the present study, MAPK gene (RmMAPK) was first cloned and characterized from Antarctic sea ice yeast R. mucilaginosa AN5. The full length of the RmMAPK gene is 1086 bp and encodes a 361 amino acids protein with a predicted molecular mass of 40.9 kDa and a pI of 5.25. The RmMAPK contains 11 MAPK conserved subdomains and the phosphorylation motif TGY located in the activation loop of the kinase. Quantitative real-time PCR and western blot assay revealed that the expression and phosphorylation level of RmMAPK up-regulated rapidly and significantly when yeast cells were subjected to low temperature (4 °C), high salinity (120‰ NaCl) and heavy metal (2 mmol/L CuCl₂).

CONCLUSIONS

All data suggested that the MAPK cascades might act as a key function in response to extreme stresses, such as low temperature, high salinity and heavy metal.

Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress

Cold stress causes major losses to sugarcane production, yet the precise molecular mechanisms that cause losses due to cold stress are not well-understood. To survey miRNAs and genes involved in cold tolerance, RNA-seq, miRNA-seq, and integration analyses were performed on Saccharum spontaneum. Results showed that a total of 118,015 genes and 6,034 of these differentially expressed genes (DEGs) were screened. Protein–protein interaction (PPI) analyses revealed that ABA signaling via protein phosphatase 2Cs was the most important signal transduction pathway and late embryogenesis abundant protein was the hub protein associated with adaptation to cold stress. Furthermore, a total of 856 miRNAs were identified in this study and 109 of them were differentially expressed in sugarcane responding to cold stress. Most importantly, the miRNA–gene regulatory networks suggested the complex post-transcriptional regulation in sugarcane under cold stress, including 10 miRNAs−42 genes, 16 miRNAs−70 genes, and three miRNAs−18 genes in CT vs. LT0.5, CT vs. LT1, and CT0.5 vs. LT1, respectively. Specifically, key regulators from 16 genes encoding laccase were targeted by novel-Chr4C_47059 and Novel-Chr4A_40498, while five LRR-RLK genes were targeted by Novel-Chr6B_65233 and Novel-Chr5D_60023, 19 PPR repeat proteins by Novel-Chr5C_57213 and Novel-Chr5D_58065. Our findings suggested that these miRNAs and cell wall-related genes played vital regulatory roles in the responses of sugarcane to cold stress. Overall, the results of this study provide insights into the transcriptional and post-transcriptional regulatory network underlying the responses of sugarcane to cold stress.

Genotoxic effects and proteomic analysis on Allium cepa var. agrogarum L. root cells under Pb stress

Ionic lead (Pb) in the environment has accumulated due to anthropogenic activities, causing a potential threat to plants and plant consumers. We conducted this study to reveal the molecular mechanism of Pb stress response in plants. The effects of Pb (5.0 and 15.0 μM) on mitosis, DNA replication, gene expression and proteins in root-tip cells of Allium cepa var. agrogarum L. were addressed. The results indicated that root growth was inhibited dramatically in Pb treatment groups. Chromosomal aberrations were observed and the mitotic index decreased during Pb treatments at different concentrations. The accumulation of reactive oxygen species (ROS) in onion roots was induced by Pb stress. Pb increased DNA damage and suppressed cell cycle progression. The above toxic effects got more serious with increasing Pb concentration and prolonging exposure time. A total of 17 proteins were expressed differentially between control and Pb exposure groups. Under Pb treatment, the decreased expression of Anx D1 indicated decreased defensive response; the decreased expression of SHMT1 indicated decreased respiration; the decreased expression of COMT2 indicated decreased response of other funtions; the increased expression of NDPK indicated increased transcription and protein synthesis; the increased expression of PR1 and CHI1 indicated increased pathogen invasion; the increased expression of ORC5 and MPK5 indicated the reduced DNA replicating activity; the decreased expression of POLD1 indicated the reduced DNA repair activity. Our results provide new insights at the proteomic level into the Pb-induced responses, defensive responses and toxic effects, and provide new molecular markers of the early events of plant responses to Pb toxicity.