Proteomic analysis of sugar beet apomictic monosomic addition line M14

Comparative Ubiquitination Proteomics Revealed the Salt Tolerance Mechanism in Sugar Beet Monomeric Additional Line M14

Post-translational modifications (PTMs) are important molecular processes that regulate organismal responses to different stresses. Ubiquitination modification is not only involved in human health but also plays crucial roles in plant growth, development, and responses to environmental stresses. In this study, we investigated the ubiquitination proteome changes in the salt-tolerant sugar beet monomeric additional line M14 under salt stress treatments. Based on the expression of the key genes of the ubiquitination system and the ubiquitination-modified proteins before and after salt stress, 30 min of 200 mM NaCl treatment and 6 h of 400 mM NaCl treatment were selected as time points. Through label-free proteomics, 4711 and 3607 proteins were identified in plants treated with 200 mM NaCl and 400 mM NaCl, respectively. Among them, 611 and 380 proteins were ubiquitinated, with 1085 and 625 ubiquitination sites, in the two salt stress conditions, respectively. A quantitative analysis revealed that 70 ubiquitinated proteins increased and 47 ubiquitinated proteins decreased. At the total protein level, 42 were induced and 20 were repressed with 200 mM NaCl, while 28 were induced and 27 were repressed with 400 mM NaCl. Gene ontology, KEGG pathway, protein interaction, and PTM crosstalk analyses were performed using the differentially ubiquitinated proteins. The differentially ubiquitinated proteins were mainly involved in cellular transcription and translation processes, signal transduction, metabolic pathways, and the ubiquitin/26S proteasome pathway. The uncovered ubiquitinated proteins constitute an important resource of the plant stress ubiquitinome, and they provide a theoretical basis for the marker-based molecular breeding of crops for enhanced stress tolerance.

Quantitative redox proteomics revealed molecular mechanisms of salt tolerance in the roots of sugar beet monomeric addition line M14

BACKGROUND

Salt stress is often associated with excessive production of reactive oxygen species (ROS). Oxidative stress caused by the accumulation of ROS is a major factor that negatively affects crop growth and yield. Root is the primary organ that senses and transmits the salt stress signal to the whole plant. How oxidative stress affect redox sensitive proteins in the roots is not known.

RESULTS

In this study, the redox proteome of sugar beet M14 roots under salt stress was investigated. Using iTRAQ reporters, we determined that salt stress caused significant changes in the abundance of many proteins (2305 at 20 min salt stress and 2663 at 10 min salt stress). Using iodoTMT reporters, a total of 95 redox proteins were determined to be responsive to salt stress after normalizing again total protein level changes. Notably, most of the differential redox proteins were involved in metabolism, ROS homeostasis, and stress and defense, while a small number play a role in transport, biosynthesis, signal transduction, transcription and photosynthesis. Transcription levels of 14 genes encoding the identified redox proteins were analyzed using qRT-PCR. All the genes were induced by salt stress at the transcriptional level.

CONCLUSIONS

Based on the redox proteomics results, we construct a map of the regulatory network of M14 root redox proteins in response to salt stress. This study further refines the molecular mechanism of salt resistance at the level of protein redox regulation.

Cys-SH based quantitative redox proteomics of salt induced response in sugar beet monosomic addition line M14

BACKGROUND

Salt stress is a major abiotic stress that limits plant growth, development and productivity. Studying the molecular mechanisms of salt stress tolerance may help to enhance crop productivity. Sugar beet monosomic addition line M14 exhibits tolerance to salt stress.

RESULTS

In this work, the changes in the BvM14 proteome and redox proteome induced by salt stress were analyzed using a multiplex iodoTMTRAQ double labeling quantitative proteomics approach. A total of 80 proteins were differentially expressed under salt stress. Interestingly, A total of 48 redoxed peptides were identified for 42 potential redox-regulated proteins showed differential redox change under salt stress. A large proportion of the redox proteins were involved in photosynthesis, ROS homeostasis and other pathways. For example, ribulose bisphosphate carboxylase/oxygenase activase changed in its redox state after salt treatments. In addition, three redox proteins involved in regulation of ROS homeostasis were also changed in redox states. Transcription levels of eighteen differential proteins and redox proteins were profiled. (The proteomics data generated in this study have been submitted to the ProteomeXchange and can be accessed via username: reviewer_pxd027550@ebi.ac.uk, password: q9YNM1Pe and proteomeXchange# PXD027550.) CONCLUSIONS: The results showed involvement of protein redox modifications in BvM14 salt stress response and revealed the short-term salt responsive mechanisms. The knowledge may inform marker-based breeding effort of sugar beet and other crops for stress resilience and high yield.

Mechanisms of Sugar Beet Response to Biotic and Abiotic Stresses

Sugar beet is used not only in the sugar production, but also in a wide range of industries including the production of bioethanol as a source of renewable energy, extraction of pectin and production of molasses. The red beetroot has attracted much attention as health-promoting and disease-preventing functional food. The negative effects of environmental stresses, including abiotic and biotic ones, significantly decrease the cash crop sugar beet productivity. In this paper, we outline the mechanisms of sugar beet response to biotic and abiotic stresses at the levels of physiological change, the genes' functions, transcription and translation. Regarding the physiological changes, most research has been carried out on salt and drought stress. The functions of genes from sugar beet in response to salt, cold and heavy metal stresses were mainly investigated by transgenic technologies. At the transcriptional level, the transcriptome analysis of sugar beet in response to salt, cold and biotic stresses were conducted by RNA-Seq or SSH methods. At the translational level, more than 800 differentially expressed proteins in response to salt, K⁺/Na⁺ ratio, iron deficiency and resupply and heavy metal (zinc) stress were identified by quantitative proteomics techniques. Understanding how sugar beet respond and tolerate biotic and abiotic stresses is important for boosting sugar beet productivity under these challenging conditions. In order to minimize the negative impact of these stresses, studying how the sugar beet has evolved stress coping mechanisms will provide new insights and lead to novel strategies for improving the breeding of stress-resistant sugar beet and other crops.

Advances in Understanding the Physiological and Molecular Responses of Sugar Beet to Salt Stress

Soil salinity is a major environmental stress on crop growth and productivity. A better understanding of the molecular and physiological mechanisms underlying salt tolerance will facilitate efforts to improve crop performance under salinity. Sugar beet is considered to be a salt-tolerant crop, and it is therefore a good model for studying salt acclimation in crops. Recently, many determinants of salt tolerance and regulatory mechanisms have been studied by using physiological and 'omics approaches. This review provides an overview of recent research advances regarding sugar beet response and tolerance to salt stress. We summarize the physiological and molecular mechanisms involved, including maintenance of ion homeostasis, accumulation of osmotic-adjustment substances, and antioxidant regulation. We focus on progress in deciphering the mechanisms using 'omic technologies and describe the key candidate genes involved in sugar beet salt tolerance. Understanding the response and tolerance of sugar beet to salt stress will enable translational application to other crops and thus will have significant impacts on agricultural sustainability and global food security.

De novo transcriptome assembly and identification of salt-responsive genes in sugar beet M14

Sugar beet (Beta vulgaris) is an important crop of sugar production in the world. Previous studies reported that sugar beet monosomic addition line M14 obtained from the intercross between Beta vulgaris L. (cultivated species) and B. corolliflora Zoss (wild species) exhibited tolerance to salt (up to 0.5 M NaCl) stress. To estimate a broad spectrum of genes involved in the M14 salt tolerance will help elucidate the molecular mechanisms underlying salt stress. Comparative transcriptomics was performed to monitor genes differentially expressed in the leaf and root samples of the sugar beet M14 seedlings treated with 0, 200 and 400 mM NaCl, respectively. Digital gene expression revealed that 3856 unigenes in leaves and 7157 unigenes in roots were differentially expressed under salt stress. Enrichment analysis of the differentially expressed genes based on GO and KEGG databases showed that in both leaves and roots genes related to regulation of redox balance, signal transduction, and protein phosphorylation were differentially expressed. Comparison of gene expression in the leaf and root samples treated with 200 and 400 mM NaCl revealed different mechanisms for coping with salt stress. In addition, the expression levels of nine unigenes in the reactive oxygen species (ROS) scavenging system exhibited significant differences in the leaves and roots. Our transcriptomics results have provided new insights into the salt-stress responses in the leaves and roots of sugar beet.

Metabolite profiling at the cellular and subcellular level reveals metabolites associated with salinity tolerance in sugar beet

Sugar beet is among the most salt-tolerant crops. This study aimed to investigate the metabolic adaptation of sugar beet to salt stress at the cellular and subcellular levels. Seedlings were grown hydroponically and subjected to stepwise increases in salt stress up to 300 mM NaCl. Highly enriched fractions of chloroplasts were obtained by non-aqueous fractionation using organic solvents. Total leaf metabolites and metabolites in chloroplasts were profiled at 3 h and 14 d after reaching the maximum salinity stress of 300 mM NaCl. Metabolite profiling by gas chromatography-mass spectrometry (GC-MS) resulted in the identification of a total of 83 metabolites in leaves and chloroplasts under control and stress conditions. There was a lower abundance of Calvin cycle metabolites under salinity whereas there was a higher abundance of oxidative pentose phosphate cycle metabolites such as 6-phosphogluconate. Accumulation of ribose-5-phosphate and ribulose-5-phosphate coincided with limitation of carbon fixation by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Increases in glycolate and serine levels indicated that photorespiratory metabolism was stimulated in salt-stressed sugar beet. Compatible solutes such as proline, mannitol, and putrescine accumulated mostly outside the chloroplasts. Within the chloroplast, putrescine had the highest relative level and probably assisted in the acclimation of sugar beet to high salinity stress. The results provide new information on the contribution of chloroplasts and the extra-chloroplast space to salinity tolerance via metabolic adjustment in sugar beet.

Overexpression of S-Adenosyl-l-Methionine Synthetase 2 from Sugar Beet M14 Increased Arabidopsis Tolerance to Salt and Oxidative Stress

The sugar beet monosomic addition line M14 is a unique germplasm that contains genetic materials from Beta vulgaris L. and Beta corolliflora Zoss, and shows tolerance to salt stress. Our study focuses on exploring the molecular mechanism of the salt tolerance of the sugar beet M14. In order to identify differentially expressed genes in M14 under salt stress, a subtractive cDNA library was generated by suppression subtractive hybridization (SSH). A total of 36 unique sequences were identified in the library and their putative functions were analyzed. One of the genes, S-adenosylmethionine synthetase (SAMS), is the key enzyme involved in the biosynthesis of S-adenosylmethionine (SAM), a precursor of polyamines. To determine the potential role of SAMS in salt tolerance, we isolated BvM14-SAMS2 from the salt-tolerant sugar beet M14. The expression of BvM14-SAMS2 in leaves and roots was greatly induced by salt stress. Overexpression of BvM14-SAMS2 in Arabidopsis resulted in enhanced salt and H₂O₂ tolerance. Furthermore, we obtained a knock-down T-DNA insertion mutant of AtSAMS3, which shares the highest homology with BvM14-SAMS2. Interestingly, the mutant atsam3 showed sensitivity to salt and H₂O₂ stress. We also found that the antioxidant system and polyamine metabolism play an important role in salt and H₂O₂ tolerance in the BvM14-SAMS2-overexpressed plants. To our knowledge, the function of the sugar beet SAMS has not been reported before. Our results have provided new insights into SAMS functions in sugar beet.

Quantitative proteomics and phosphoproteomics of sugar beet monosomic addition line M14 in response to salt stress

Salinity is a major abiotic stress affecting plant growth, development and agriculture productivity. Understanding the molecular mechanisms of salt stress tolerance will provide valuable information for effective crop engineering and breeding. Sugar beet monosomic addition line M14 obtained from the intercross between Beta vulgaris L. and Beta corolliflora Zoss exhibits tolerance to salt stress. In this study, the changes in the M14 proteome and phosphoproteome induced by salt stress were analyzed. We report the characteristics of the M14 plants under 0, 200, and 400mM NaCl using label-free quantitative proteomics approaches. Protein samples were subjected to total proteome profiling using LC-MS/MS and phosphopeptide enrichment to identify phosphopeptides and phosphoproteins. A total of 2182 proteins were identified and 114 proteins showed differential levels under salt stress. Interestingly, 189 phosphoproteins exhibited significant changes at the phosphorylation level under salt stress. Several signaling components associated with salt stress were found, e.g. 14-3-3 and mitogen-activated protein kinases (MAPK). Fifteen differential phosphoproteins and proteins involved in signal transduction were tested at the transcriptional level. The results revealed the short-term salt responsive mechanisms of the special sugar beet M14 line using label-free quantitative phosphoproteomics.

BIOLOGICAL SIGNIFICANCE

Sugar beet monosomic addition line M14 is a special germplasm with salt stress tolerance. Analysis of the M14 proteome and phosphoproteome under salt stress has provided insight into specific response mechanisms underlying salt stress tolerance. Reversible protein phosphorylation regulates a wide range of cellular processes such as transmembrane signaling, intracellular amplification of signals, and cell-cycle control. This study has identified significantly changed proteins and phosphoproteins, and determined their potential relevance to salt stress response. The knowledge gained can be potentially applied to improving crop salt tolerance.

OMICS Technologies and Applications in Sugar Beet

Sugar beet is a species of the Chenopodiaceae family. It is an important sugar crop that supplies approximately 35% of the sugar in the world. Sugar beet M14 line is a unique germplasm that contains genetic materials from Beta vulgaris L. and Beta corolliflora Zoss. And exhibits tolerance to salt stress. In this review, we have summarized OMICS technologies and applications in sugar beet including M14 for identification of novel genes, proteins related to biotic and abiotic stresses, apomixes and metabolites related to energy and food. An OMICS overview for the discovery of novel genes, proteins and metabolites in sugar beet has helped us understand the complex mechanisms underlying many processes such as apomixes, tolerance to biotic and abiotic stresses. The knowledge gained is valuable for improving the tolerance of sugar beet and other crops to biotic and abiotic stresses as well as for enhancing the yield of sugar beet for energy and food production.

Salt stress response of membrane proteome of sugar beet monosomic addition line M14

Understanding how plants respond to and tolerate salt stress is important for engineering and breeding effort to boost plant productivity and bioenergy in an ever challenging environment. Sugar beet M14 line is a unique germplasm that contains genetic materials from Beta vulgaris L. and Beta corolliflora Zoss, and it exhibits tolerance to salt stress. Here we report the changes in membrane proteome of the M14 plants in response to salt stress (0, 200, 400mM NaCl) using an iTRAQ two-dimensional LC-MS/MS technology for quantitative proteomic analysis. In total, 274 proteins, mostly membrane proteins, were identified, and 50 proteins exhibited differential protein level changes, with 40 proteins increased and 10 decreased. The proteins were mainly involved in transport, metabolism, protein synthesis, photosynthesis, protein folding and degradation, signal transduction, stress and defense, energy, and cell structure. These results have revealed interesting mechanisms underlying the M14 response and tolerance to salt stress.

BIOLOGICAL SIGNIFICANCE

Sugar beet monosomic addition line M14 is a special variety with salt stress tolerance. Analysis of the M14 membrane proteome under salt stress may provide useful information regarding specific adaptive mechanisms underlying salt stress tolerance. Membrane proteins are known to play critical roles in salt stress signaling and adaptation. The purpose of this study was to identify significantly changed membrane proteins and determine their possible relevance to salt tolerance. The proteomic analysis of the M14 line revealed important molecular mechanisms that can be potentially applied to improving crop salt tolerance. This article is part of a Special Issue entitled: Proteomics in India.

Protein extraction from plant tissues for 2DE and its application in proteomic analysis

Plant tissues contain large amounts of secondary compounds that significantly interfere with protein extraction and 2DE analysis. Thus, sample preparation is a crucial step prior to 2DE in plant proteomics. This tutorial highlights the guidelines that need to be followed to perform an adequate total protein extraction before 2DE in plant proteomics. We briefly describe the history, development, and feature of major sample preparation methods for the 2DE analysis of plant tissues, that is, trichloroacetic acid/acetone precipitation and phenol extraction. We introduce the interfering compounds in plant tissues and the general guidelines for tissue disruption, protein precipitation and resolubilization. We describe in details the advantages, limitations, and application of the trichloroacetic acid/acetone precipitation and phenol extraction methods to enable the readers to select the appropriate method for a specific species, tissue, or cell type. The current applications of the sample preparation methods in plant proteomics in the literature are analyzed. A comparative proteomic analysis between male and female plants of Pistacia chinensis is used as an example to represent the sample preparation methodology in 2DE-based proteomics. Finally, the current limitations and future development of these sample preparation methods are discussed. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP17).

Sugar beet M14 glyoxalase I gene can enhance plant tolerance to abiotic stresses

Glyoxalase I is the first enzyme of the glyoxalase system that can detoxify methylglyoxal, a cytotoxic compound increased rapidly under stress conditions. Here we report cloning and characterization of a glyoxalase I from sugar beet M14 line (an interspecific hybrid between a wild species Beta corolliflora Zoss and a cultivated species B. vulgaris L). The full-length gene BvM14-glyoxalase I has 1,449 bp in length with an open reading frame of 1,065 bp encoding 354 amino acids. Sequence analysis shows the conserved glyoxalase I domains, metal and glutathione binding sites and secondary structure (α-helixes and β-sheets). The BvM14-glyoxalase I gene was ubiquitously expressed in different tissues of sugar beet M14 line and up-regulated in response to salt, mannitol and oxidative stresses. Heterologous expression of BvM14-glyoxalase I could increase E. coli tolerance to methylglyoxal. Transgenic tobacco plants constitutively expressing BvM14-glyoxalase I were generated. Both leaf discs and seedlings showed significant tolerance to methylglyoxal, salt, mannitol and H2O2. These results suggest an important role of BvM14-glyoxalase I in cellular detoxification and tolerance to abiotic stresses.

Salt stress induced proteome and transcriptome changes in sugar beet monosomic addition line M14

Sugar beet monosomic addition line M14 displays interesting phenotypes such as apomixis and salt stress tolerance. Here we reported proteomic and transcriptomic analysis of M14 leaves and roots under 500mM NaCl treatment for seven days. Proteins from control and treated samples were extracted and separated using two-dimensional difference gel electrophoresis (2D-DIGE). A total of 40 protein spots from leaf gels and 36 protein spots from root gels exhibited significant changes. Using mass spectrometry and database searching, 38 unique proteins in leaves and 29 unique proteins in roots were identified. The proteins included those involved in metabolism, protein folding, photosynthesis, and protein degradation. In addition, cDNA libraries of differentially expressed genes were constructed using suppression subtractive hybridization (SSH). Fifty-eight unigenes including 14 singletons and 44 contigs were obtained. Some salt-responsive genes were identified to function in metabolism, photosynthesis, stress and defense, energy, protein synthesis and protein degradation. This research has revealed candidate genes and proteins for detailed functional characterization, and set the stage for further investigation of the salt tolerance mechanisms in sugar beet.

Identification of a sugar beet BvM14-MADS box gene through differential gene expression analysis of monosomic addition line M14

Monosomic addition line M14 carrying an additional chromosome 9 from Beta corolliflora Zosimovic ex Buttler was obtained through hybridization between the wild species B. corolliflora and a cultivated species Beta vulgaris L. var Saccharifera Alef. The M14 line showed diplosporic reproduction and stress tolerance. To identify differentially expressed genes in M14, a subtractive cDNA library was prepared by suppression subtractive hybridization (SSH) between M14 (2n=18+1) and B. vulgaris (2n=18). A total of 190 unique sequences were identified in the library and their putative functions were analyzed using Gene Ontology (GO). One of the genes, designated as BvM14-MADS box, encodes a MADS box transcription factor. It was cloned from M14 and over-expressed in transgenic tobacco plants. Interestingly, this gene was located on chromosome 2 of B. vulgaris, not on the additional chromosome 9. Overexpression of BvM14-MADS box led to significant phenotypic changes in tobacco. The differential expression of BvM14-MADS box gene in M14 may be caused by the interaction between the additional chromosome 9 from B. corolliflora and the B. vulgaris chromosomes in M14.