Molecular characterization of an ethephon-induced Hsp70 involved in high and low-temperature responses in Hevea brasiliensis

Genome-wide analysis of Hsp40 and Hsp70 gene family in four cotton species provides insights into their involvement in response to Verticillium dahliae and abiotic stress

Introduction: Cotton is an important economic crop to provide natural fibers as raw materials to textile industry, and is significantly affected by biotic and abiotic stress during the whole growth stage, in which Verticillium wilt (VW) caused by Verticillium dahliae is one of the most destructive disease to lead to a significant yield reduction. Heat shock proteins (Hsps) are important molecular chaperones, and play crucial roles in plant growth, development, resistance to biotic and abiotic stress. Hsp40 and Hsp70 are two key Hsps in cell chaperone network, however, the function and regulatory mechanism of Hsp40 and Hsp70 members in VW resistance and abiotic stress in cotton are largely unknown. Methods and Results: Herein, a systematic and comprehensive analysis of Hsp40s and Hsp70s in four cotton species of Gossypium arboretum, G. raimondii, G. hirsutum, and G. barbadense were performed. A total of 291 Hsp40s and 171 Hsp70s identified in four Gossypium species. Sequence analysis revealed that all Hsp40 proteins contained J domain that provides the binding sites to Hsp70. Protein-protein interaction prediction analysis displayed that GhHsp40-55 might interact with GhHsp70-2 and GhHsp70-13, suggesting their potential function as protein complex. Promoter cis-acting element analysis demonstrated that multiple cis-elements related to disease and stress response consists in GhHsp40 and GhHsp70 promoters. Further expression analysis showed that eight GhHsp40s (Hsp40-2,4,8,11,20,23,53,55) and seven GhHsp70s (Hsp70-2,3,6,8,13,19,22) were up-regulated after V. dahliae infection. In addition, five GhHsp40s (Hsp40-2,8,11,53,55) and four GhHsp70s (Hsp70-3,6,8,13) were up-regulated after salt treatment, six GhHsp40s (Hsp40-4,11,20,23) and three GhHsp70s (Hsp70-2,8,19) were up-regulated after drought treatment, four GhHsp40s (Hsp40-2,11,20,23) and four GhHsp70s (Hsp70-3,6,19,22) were up-regulated after temperature treatment, suggesting these Hsps have possible important function in the process of abiotic stress response. Discussion: Our results lay a foundation for understanding the function of Hsp40 and Hsp70 in the resistance against V. dahliae and abiotic stress, and elucidating the regulatory mechanism of the protein complex, evolution and molecular mechanism under stress.

Comprehensive Profiling of Paper Mulberry (Broussonetia papyrifera) Crotonylome Reveals the Significance of Lysine Crotonylation in Young Leaves

Lysine crotonylation is a newly discovered and reversible posttranslational modification involved in various biological processes, especially metabolism regulation. A total of 5159 lysine crotonylation sites in 2272 protein groups were identified. Twenty-seven motifs were found to be the preferred amino acid sequences for crotonylation sites. Functional annotation analyses revealed that most crotonylated proteins play important roles in metabolic processes and photosynthesis. Bioinformatics analysis suggested that lysine crotonylation preferentially targets a variety of important biological processes, including ribosome, glyoxylate and dicarboxylate metabolism, carbon fixation in photosynthetic organisms, proteasome and the TCA cycle, indicating lysine crotonylation is involved in the common mechanism of metabolic regulation. A protein interaction network analysis revealed that diverse interactions are modulated by protein crotonylation. These results suggest that lysine crotonylation is involved in a variety of biological processes. HSP70 is a crucial protein involved in protecting plant cells and tissues from thermal or abiotic stress responses, and HSP70 protein was found to be crotonylated in paper mulberry. This systematic analysis provides the first comprehensive analysis of lysine crotonylation in paper mulberry and provides important resources for further study on the regulatory mechanism and function of the lysine crotonylated proteome.

Genome-wide analysis of Hsp70 and Hsp100 gene families in Ziziphus jujuba

The Ziziphus species are naturally tolerant to a range of abiotic stresses. Therefore, it is expected that they are an enriched source of genes conferring stress tolerance. Heat shock proteins (Hsps) play a significant role in plants in imparting tolerance against abiotic stress conditions. To get an insight into potential Hsp function in Ziziphus, we performed a genome-wide analysis and expression study of Hsp70 and Hsp100 gene families in Ziziphus jujuba. We identified 21 and 6 genes of the ZjHsp70 and ZjHsp100 families, respectively. Physiochemical properties, chromosomal location, gene structure, motifs, and protein domain organization were analysed for structural and functional characterization. We identified the contribution of tandem and segmental gene duplications in expansions of ZjHsp70s and ZjHsp100s in Z. jujuba. Promoter analysis suggested that ZjHsp70s and ZjHsp100s perform diverse functions related to abiotic stress. Furthermore, expression analyses revealed that most of the Z. jujuba Hsp genes are differentially expressed in response to heat, drought, and salinity stress. Our analyses suggested ZjHsp70-3, ZjHsp70-5, ZjHsp70-6, ZjHsp70-16, ZjHsp70-17, ZjHsp70-20, ZjHsp100-1, ZjHsp100-2, and ZjHsp100-3 are potential candidates for further functional analysis and with regard to breeding new more resilient strains. The present analysis laid the foundation for understanding the molecular mechanism of Hsps70 and Hsp100 gene families regulating abiotic stress tolerance in Z. jujuba.

Genome-Wide Analysis of HSP70 Family Protein in Vigna radiata and Coexpression Analysis Under Abiotic and Biotic Stress

Heat shock protein 70 (Hsp70), a 70-kDa protein, also known as a molecular chaperone, is highly conserved. It plays a major role in cellular functions such as protein folding, regulation of protein degradation, translocation of proteins across membranes, receptor signaling, and protein assembly or disassembly. Vigna radiata is an important legume crop with available whole-genome sequence, but no such study on the HSP70 family is reported. A total of 32 V. radiate HSP70s (Vr-HSP70s) were identified and described. They are phylogenetically clustered into four subgroups. Vr-HSP70s show variations in intron/exon organization. This indicates that introns may play an essential role in gene regulating. The coexpression analysis of Vr-HSP70s revealed that these genes were involved in both abiotic and biotic stresses. Three cytoplasmic hub genes namely Vr-HSP70-C-14, Vr-HSP70-C-29, and Vr-HSP70-C-30 were found common in both stresses. Our findings provide directions for future studies to dissect functional analysis of Vr-HSP70s in response to abiotic and biotic stresses.

Quercetin attenuates hypertension induced by sodium fluoride via reduction in oxidative stress and modulation of HSP 70/ERK/PPARγ signaling pathways

Hypertension is one of the silent killers in the world with high mortality and morbidity. The exposure of humans and animals to fluoride and/or fluoride containing compounds is almost inevitable. This study investigated the modulatory effects of quercetin on sodium fluoride (NaF)-induced hypertension and cardiovascular complications. Forty male rats were randomly separated into four groups (n =10). Group A animals served as the control, rats in Group B were exposed to 300 ppm of NaF, Groups C and D animals were exposed to 300 ppm of NaF along with quercetin orally at 50 mg/kg and 100 mg/kg orally by gavage, while NaF was administered in drinking water, respectively, for a week. Administration of NaF caused severe hypertension as indicated with significant increases in the systolic, diastolic, and mean arterial blood pressure, together with prolonged ventricular depolarization (QRS) and the time between the start of the Q wave and the end of the T wave in the heart's electrical cycle (QT) intervals when compared with controls. NaF significantly decreased the activities of antioxidant enzymes, caused increase in markers of oxidative stress and renal damage when compared with controls. Immunohistochemical staining revealed lower expressions of Hsp70, ERK, and PPARγ in the heart, kidney, and aorta of rats-administered NaF relative to the controls. Together, quercetin co-treatment with NaF restored blood pressure, normalized QRS interval, and improved antioxidant defense system. © 2018 BioFactors, 44(5):465-479, 2018.

Comparative transcriptome analysis reveals phytohormone signalings, heat shock module and ROS scavenger mediate the cold-tolerance of rubber tree

Two contrasting cold response rubber tree clones, the cold-resistant ‘93-114’ and cold-sensitive ‘Reken501’, were subject to a global transcriptome response assessing via high-throughput RNA-seq technique and comprehensive bioinformatics analysis using the referenced rubber tree genome with the purpose of exploring the potential molecular cues underlying the tolerance of rubber trees to cold stress. As a result, a total of 1919 genes had significantly higher expression, while 2929 genes had significantly lower expression in ‘93–114’ than in ‘Reken501’ without cold stress. Upon cold stress, the numbers of genes with significantly higher expression decreased to 1501 at 1 h treatment and to 1285 at 24 h treatment in ‘93–114’ than that of ‘Reken501’, conversely, the numbers of genes with significantly lower expression increased to 7567 at 1 h treatment and to 5482 at 24 h treatment. Functional annotation of the differentially expressed genes between ‘93–114’ and ‘Reken501’ suggests that down-regulation of auxin and ethylene signaling and activation of heat shock module and ROS scavengers is a primary strategy for H. brasiliensis to cope with cold stress. Our identified vital differentially expressed genes may be beneficial for elucidation of the molecular mechanisms underlying cold tolerance and for genetic improvement of H. brasiliensis clones.

Comparative Transcriptome Analysis of Latex Reveals Molecular Mechanisms Underlying Increased Rubber Yield in Hevea brasiliensis Self-Rooting Juvenile Clones

Rubber tree (Hevea brasiliensis) self-rooting juvenile clones (JCs) are promising planting materials for rubber production. In a comparative trial between self-rooting JCs and donor clones (DCs), self-rooting JCs exhibited better performance in rubber yield. To study the molecular mechanism associated with higher rubber yield in self-rooting JCs, we sequenced and comparatively analyzed the latex of rubber tree self-rooting JCs and DCs at the transcriptome level. Total raw reads of 34,632,012 and 35,913,020 bp were obtained from the library of self-rooting JCs and DCs, respectively, by using Illumina HiSeq 2000 sequencing technology. De novo assemblies yielded 54689 unigenes from the library of self-rooting JCs and DCs. Among 54689 genes, 1716 genes were identified as differentially expressed between self-rooting JCs and DCs via comparative transcript profiling. Functional analysis showed that the genes related to the mass of categories were differentially enriched between the two clones. Several genes involved in carbohydrate metabolism, hormone metabolism and reactive oxygen species scavenging were up-regulated in self-rooting JCs, suggesting that the self-rooting JCs provide sufficient molecular basis for the increased rubber yielding, especially in the aspects of improved latex metabolisms and latex flow. Some genes encoding epigenetic modification enzymes were also differentially expressed between self-rooting JCs and DCs. Epigenetic modifications may lead to gene differential expression between self-rooting JCs and DCs. These data will provide new cues to understand the molecular mechanism underlying the improved rubber yield of H. brasiliensis self-rooting clones.

HbMADS4, a MADS-box Transcription Factor from Hevea brasiliensis, Negatively Regulates HbSRPP

In plants MADS-box transcription factors (TFs) play important roles in growth and development. However, no plant MADS-box gene has been identified to have a function related to secondary metabolites regulation. Here, a MADS-box TF gene, designated as HbMADS4, was isolated from Hevea brasiliensis by the yeast one-hybrid experiment to screen the latex cDNA library using the promoter of the gene encoding H. brasiliensis small rubber particle protein (HbSRPP) as bait. HbMADS4 was 984-bp containing 633-bp open reading frame encoding a deduced protein of 230 amino acid residues with a typical conserved MADS-box motif at the N terminus. HbMADS4 was preferentially expressed in the latex, but little expression was detected in the leaves, flowers, and roots. Its expression was inducible by methyl jasmonate and ethylene. Furthermore, transient over-expression and over-expression of HbMADS4 in transgenic tobacco plants significantly suppressed the activity of the HbSRP promoter. Altogether, it is proposed that HbMADS4 is a negative regulator of HbSRPP which participates in the biosynthesis of natural rubber.

Overexpression of MuHSP70 gene from Macrotyloma uniflorum confers multiple abiotic stress tolerance in transgenic Arabidopsis thaliana

A 70-KD heat shock protein (HSP70) is one of the most conserved chaperones. It is involved in de novo protein folding and prevents the aggregation of unfolded proteins under lethal environmental factors. The purpose of this study is to characterise a MuHSP70 from horsegram (Macrotyloma uniflorum) and elucidating its role in stress tolerance of plants. A MuHSP70 was cloned and characterised from a natural drought stress tolerant HPK4 variety of horsegram (M. uniflorum). For functional characterization, MuHSP70 was overexpressed in transgenic Arabidopsis. Overexpression of MuHSP70 was found to provide tolerance to the transgenic Arabidopsis against various stresses such as heat, cold, drought, salinity and oxidative stress. MuHSP70 transgenics were observed to maintain the shoot biomass, root length, relative water content, and chlorophyll content during exposure to multi-stresses relative to non-transgenic control. Transgenic lines have further shown the reduced levels of MDA, H2O2, and proteolytic activity. Together, these findings suggest that overexpression of MuHSP70 plays an important role in improving abiotic stress tolerance and could be a crucial candidate gene for exploration in crop improvement program.

Genome-wide analysis and expression profiling under heat and drought treatments of HSP70 gene family in soybean (Glycine max L.)

Heat shock proteins (HSPs) perform a fundamental role in protecting plants against abiotic stresses. Previous studies have made great efforts in the functional analysis of individual family members, but there has not yet been an overall analysis or expression profiling of the HSP70 gene family in soybeans (Glycine max L.). In this study, an investigation of the soybean genome revealed 61 putative HSP70 genes, which were evaluated. These genes were classified into eight sub-families, denoted I-VIII, based on a phylogenetic analysis. In each sub-family, the constituent parts of the gene structure and motif were relatively conserved. These GmHSP70 genes were distributed unequally on 17 of the 20 chromosomes. The analysis of the expression profiles showed that 53 of the 61 GmHSP70 genes were differentially expressed across the 14 tissues. However, most of the GmHSP70s were differentially expressed in a tissue-specific expression pattern. Furthermore, the expression of some of the duplicate genes was partially redundant, while others showed functional diversity. The quantitative real-time PCR (qRT-PCR) analysis of the 61 soybean HSP70 genes confirmed their stress-inducible expression patterns under both drought and heat stress. These findings provide a thorough overview of the evolution and modification of the GmHSP70 gene family, which will help to determine the functional characteristics of the HSP70 genes in soybean growth and development.

Characterization of CaHsp70-1, a pepper heat-shock protein gene in response to heat stress and some regulation exogenous substances in Capsicum annuum L

Pepper (Capsicum annuum L.) is sensitive to heat stress (HS). Heat shock proteins 70 (Hsp70s) play a crucial role in protecting plant cells against HS and control varies characters in different plants. However, CaHsp70-1 gene was not well characterized in pepper. In this study, CaHsp70-1 was cloned from the pepper thermotolerant line R9, which encoded a protein of 652 amino acids, with a molecular weight of 71.54 kDa and an isoelectric point of 5.20. CaHsp70-1 belongs to the cytosolic Hsp70 subgroup, and best matched with tomato SlHsp70. CaHsp70-1 was highly induced in root, stem, leaf and flower in R9 with HS treatment (40 °C for 2 h). In both thermosensitive line B6 and thermotolerant line R9, CaHsp70-1 significantly increased after 0.5 h of HS (40 °C), and maintained in a higher level after 4 h HS. The expression of CaHsp70-1 induced by CaCl₂, H₂O₂ and putrescine (Put) under HS were difference between B6 and R9 lines. The different expression patterns may be related to the differences in promoters of CaHsp70-1 from the two lines. These results suggest that CaHsp70-1 as a member of cytosolic Hsp70 subgroup, may be involved in HS defense response via a signal transduction pathway contained Ca²⁺, H₂O₂ and Put.

Transcriptome profile reveals heat response mechanism at molecular and metabolic levels in rice flag leaf

Flag leaf is one of the key photosynthesis organs during rice reproductive stage. A time course microarray analysis of rice flag leaf was done after 40°C treatment for 0 min, 20 min, 60 min, 2h, 4h, and 8h. The identified significant heat responsive genes were mainly involved in transcriptional regulation, transport, protein binding, antioxidant, and stress response. KMC analysis discovered the time-dependent gene expression pattern under heat. MapMan analysis demonstrated that, under heat treatment, Hsp genes and genes involved in glycolysis and ubiquitin-proteasome were enhanced, and genes involved in TCA, carotenoid, dihydroflavonol and anthocyanin metabolisms and light-reaction in the photosynthesis were widely repressed. Meanwhile, some rate-limiting enzyme genes in shikimate, lignin, and mevalonic acid metabolisms were up-regulated, revealing the importance of maintaining specific secondary metabolites under heat stress. The present study increased our understanding of heat response in rice flag leaf and provided good candidate genes for crop improvement.

Expression profile in rice panicle: insights into heat response mechanism at reproductive stage

Rice at reproductive stage is more sensitive to environmental changes, and little is known about the mechanism of heat response in rice panicle. Here, using rice microarray, we provided a time course gene expression profile of rice panicle at anther developmental stage 8 after 40°C treatment for 0 min, 20 min, 60 min, 2 h, 4 h, and 8 h. The identified differentially expressed genes were mainly involved in transcriptional regulation, transport, cellular homeostasis, and stress response. The predominant transcription factor gene families responsive to heat stress were Hsf, NAC, AP2/ERF, WRKY, MYB, and C₂H₂. KMC analysis discovered the time-dependent gene expression pattern under heat stress. The motif co-occurrence analysis on the promoters of genes from an early up-regulated cluster showed the important roles of GCC box, HSE, ABRE, and CE3 in response to heat stress. The regulation model central to ROS combined with transcriptome and ROS quantification data in rice panicle indicated the great importance to maintain ROS balance and the existence of wide cross-talk in heat response. The present study increased our understanding of the heat response in rice panicle and provided good candidate genes for crop improvement.

De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.)

Background

In rubber tree, bark is one of important agricultural and biological organs. However, the molecular mechanism involved in the bark formation and development in rubber tree remains largely unknown, which is at least partially due to lack of bark transcriptomic and genomic information. Therefore, it is necessary to carried out high-throughput transcriptome sequencing of rubber tree bark to generate enormous transcript sequences for the functional characterization and molecular marker development.

Results

In this study, more than 30 million sequencing reads were generated using Illumina paired-end sequencing technology. In total, 22,756 unigenes with an average length of 485 bp were obtained with de novo assembly. The similarity search indicated that 16,520 and 12,558 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Among these annotated unigenes, 6,867 and 5,559 unigenes were separately assigned to Gene Ontology (GO) and Clusters of Orthologous Group (COG). When 22,756 unigenes searched against the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database, 12,097 unigenes were assigned to 5 main categories including 123 KEGG pathways. Among the main KEGG categories, metabolism was the biggest category (9,043, 74.75%), suggesting the active metabolic processes in rubber tree bark. In addition, a total of 39,257 EST-SSRs were identified from 22,756 unigenes, and the characterizations of EST-SSRs were further analyzed in rubber tree. 110 potential marker sites were randomly selected to validate the assembly quality and develop EST-SSR markers. Among 13 Hevea germplasms, PCR success rate and polymorphism rate of 110 markers were separately 96.36% and 55.45% in this study.

Conclusion

By assembling and analyzing de novo transcriptome sequencing data, we reported the comprehensive functional characterization of rubber tree bark. This research generated a substantial fraction of rubber tree transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation, and microarrays development in rubber tree. The EST-SSR markers identified and developed in this study will facilitate marker-assisted selection breeding in rubber tree. Moreover, this study also supported that transcriptome analysis based on Illumina paired-end sequencing is a powerful tool for transcriptome characterization and molecular marker development in non-model species, especially those with large and complex genomes.