Primary structural features of the 20S proteasome subunits of rice (Oryza sativa)

Phylogenomic analysis of 20S proteasome gene family reveals stress-responsive patterns in rapeseed (Brassica napus L.)

The core particle represents the catalytic portions of the 26S proteasomal complex. The genes encoding α- and β-subunits play a crucial role in protecting plants against various environmental stresses by controlling the quality of newly produced proteins. The 20S proteasome gene family has already been reported in model plants such as Arabidopsis and rice; however, they have not been studied in oilseed crops such as rapeseed (Brassica napus L.). In the present study, we identified 20S proteasome genes for α- (PA) and β-subunits (PB) in B. napus through systematically performed gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 82 genes, comprising 35 BnPA and 47 BnPB of the 20S proteasome, were revealed in the B. napus genome. These genes were distributed on all 20 chromosomes of B. napus and most of these genes were duplicated on homoeologous chromosomes. The BnPA (α1-7) and BnPB (β1-7) genes were phylogenetically placed into seven clades. The pattern of expression of all the BnPA and BnPB genes was also studied using RNA-seq datasets under biotic and abiotic stress conditions. Out of 82 BnPA/PB genes, three exhibited high expression under abiotic stresses, whereas two genes were overexpressed in response to biotic stresses at both the seedling and flowering stages. Moreover, an additional eighteen genes were expressed under normal conditions. Overall, the current findings developed our understanding of the organization of the 20S proteasome genes in B. napus, and provided specific BnPA/PB genes for further functional research in response to abiotic and biotic stresses.

Development of High Yielding Glutinous Cytoplasmic Male Sterile Rice (Oryza sativa L.) Lines through CRISPR/Cas9 Based Mutagenesis of Wx and TGW6 and Proteomic Analysis of Anther

Development of high yielding and more palatable glutinous rice is an important goal in breeding and long-standing cultural interaction in Asia. In this study, the TGW6 and Wx, major genes conferring 1000 grain weight (GW) and amylose content (AC), were edited in a maintainer line by CRISPR/Cas9 technology. Four targets were assembled in pYLCRISPR/Cas9Pubi-H vector and T0 mutant plants were obtained through Agrobacterium mediated transformation with 90% mutation frequency having 28% homozygous mutations without off-target effects in three most likely sites of each target and expression level of target genes in mutant lines was significantly decreased (P < 0.01), the GW and gel consistency (GC) were increased, and the AC and gelatinization temperature (GT) were decreased significantly and grain appearance was opaque, while there was no change in starch content (SC) and other agronomic traits. Mutations were inheritable and some T1 plants were re-edited but T2 generation was completely stable. The pollen fertility status was randomly distributed, and the mutant maintainer lines were hybridized with Cytoplasmic Male Sterile (CMS) line 209A and after subsequent backcrossing the two glutinous CMS lines were obtained in BC2F1. The identified proteins from anthers of CMS and maintainer line were closely associated with transcription, metabolism, signal transduction, and protein biosynthesis. Putative mitochondrial NAD+-dependent malic enzyme was absent in CMS line which caused the pollen sterility because of insufficient energy, while upregulation of putative acetyl-CoA synthetase and Isoamylase in both lines might have strong relationship with CMS and amylose content. High yielding glutinous CMS lines will facilitate hybrid rice breeding and investigations of proteins linked to male sterility will provide the insights to complicated metabolic network in anther development.

Quantitative proteome-level analysis of paulownia witches' broom disease with methyl methane sulfonate assistance reveals diverse metabolic changes during the infection and recovery processes

Paulownia witches' broom (PaWB) disease caused by phytoplasma is a fatal disease that leads to considerable economic losses. Although there are a few reports describing studies of PaWB pathogenesis, the molecular mechanisms underlying phytoplasma pathogenicity in Paulownia trees remain uncharacterized. In this study, after building a transcriptome database containing 67,177 sequences, we used isobaric tags for relative and absolute quantification (iTRAQ) to quantify and analyze the proteome-level changes among healthy P. fortunei (PF), PaWB-infected P. fortunei (PFI), and PaWB-infected P. fortunei treated with 20 mg L^-1 or 60 mg L^-1 methyl methane sulfonate (MMS) (PFI-20 and PFI-60, respectively). A total of 2,358 proteins were identified. We investigated the proteins profiles in PF vs. PFI (infected process) and PFI-20 vs. PFI-60 (recovered process), and further found that many of the MMS-response proteins mapped to "photosynthesis" and "ribosome" pathways. Based on our comparison scheme, 36 PaWB-related proteins were revealed. Among them, 32 proteins were classified into three functional groups: (1) carbohydrate and energy metabolism, (2) protein synthesis and degradation, and (3) stress resistance. We then investigated the PaWB-related proteins involved in the infected and recovered processes, and discovered that carbohydrate and energy metabolism was inhibited, and protein synthesis and degradation decreased, as the plant responded to PaWB. Our observations may be useful for characterizing the proteome-level changes that occur at different stages of PaWB disease. The data generated in this study may serve as a valuable resource for elucidating the pathogenesis of PaWB disease during phytoplasma infection and recovery stages.

Proteomics of Durum Wheat Grain during Transition to Conservation Agriculture

Nitrogen management in combination with sustainable agronomic techniques can have a great impact on the wheat grain proteome influencing its technological quality. In this study, proteomic analyses were used to document changes in the proportion of prolamins in mature grains of the newly released Italian durum wheat cv Achille. Such an approach was applied to wheat fertilized with urea (UREA) and calcium nitrate (NITRATE), during the transition to no-till Conservation Agriculture (CA) practice in a Mediterranean environment. Results obtained in a two-years field experiment study suggest low molecular weight glutenins (LMW-GS) as the fraction particularly inducible regardless of the N-form. Quantitative analyses of LMW-GS by 2D-GE followed by protein identification by LC-ESI-MS/MS showed that the stable increase was principally due to C-type LMW-GS. The highest accumulation resulted from a physiologically healthier state of plants treated with UREA and NITRATE. Proteomic analysis on the total protein fraction during the active phase of grain filling was also performed. For both N treatments, but at different extent, an up-regulation of different classes of proteins was observed: i) enzymes involved in glycolysis and citric acid cycles which contribute to an enhanced source of energy and carbohydrates, ii) stress proteins like heat shock proteins (HSPs) and antioxidant enzymes, such as peroxidases and superoxide dismutase which protect the grain from abiotic stress during starch and storage protein synthesis. In conclusion N inputs, which combined rate with N form gave high yield and improved quality traits in the selected durum wheat cultivar. The specific up-regulation of some HSPs, antioxidant enzymes and defense proteins in the early stages of grain development and physiological indicators related to fitness traits, could be useful bio-indicators, for wheat genotype screening under more sustainable agronomic conditions, like transition phase to no-till CA in Mediterranean environments.

Proteomics of seed development, desiccation tolerance, germination and vigor

Proteomics, the large-scale study of the total complement of proteins in a given sample, has been applied to all aspects of seed biology mainly using model species such as Arabidopsis or important agricultural crops such as corn and rice. Proteins extracted from the sample have typically been separated and quantified by 2-dimensional polyacrylamide gel electrophoresis followed by liquid chromatography and mass spectrometry to identify the proteins in the gel spots. In this way, qualitative and quantitative changes in the proteome during seed development, desiccation tolerance, germination, dormancy release, vigor alteration and responses to environmental factors have all been studied. Many proteins or biological processes potentially important for each seed process have been highlighted by these studies, which greatly expands our knowledge of seed biology. Proteins that have been identified to be particularly important for at least two of the seed processes are involved in detoxification of reactive oxygen species, the cytoskeleton, glycolysis, protein biosynthesis, post-translational modifications, methionine metabolism, and late embryogenesis-abundant (LEA) proteins. It will be useful for molecular biologists and molecular plant breeders to identify and study genes encoding particularly interesting target proteins with the aim to improve the yield, stress tolerance or other critical properties of our crop species.

Comparative transcriptome analysis of the lichen-forming fungus Endocarpon pusillum elucidates its drought adaptation mechanisms

The lichen-forming fungus was isolated from the desert lichen Endocarpon pusillum that is extremely drought resistant. To understand the molecular mechanisms of drought resistance in the fungus, we employed RNA-seq and quantitative real-time PCR to compare and characterize the differentially expressed genes in pure culture at two different water levels and with that in desiccated lichen. The comparative transcriptome analysis indicated that a total of 1781 genes were differentially expressed between samples cultured under normal and PEG-induced drought stress conditions. Similar to those in drought resistance plants and non-lichenized fungi, the common drought-resistant mechanisms were differentially expressed in E. pusillum. However, the expression change of genes involved in osmotic regulation in E. pusillum is different, which might be the evidence for the feature of drought adaptation. Interestingly, different from other organisms, some genes involved in drought adaption mechanisms showed significantly different expression patterns between the presence and absence of drought stress in E. pusillum. The expression of 23 candidate stress responsive genes was further confirmed by quantitative real-time PCR using dehydrated E. pusillum lichen thalli. This study provides a valuable resource for future research on lichen-forming fungi and shall facilitate future functional studies of the specific genes related to drought resistance.

Elucidating hormonal/ROS networks during seed germination: insights and perspectives

While authors have traditionally emphasized the deleterious effects of reactive oxygen species (ROS) on seed biology, their role as signaling molecules during seed dormancy alleviation and germination is now the focus of many studies around the world. Over the last few years, studies using "-omics" technologies together with physiological and biochemical approaches have revealed that seed germination is a very complex process that depends on multiple biochemical and molecular variables. The pivotal role of phytohormones in promoting germination now appears to be interdependent with ROS metabolism, involving mitogen-activated protein kinase cascade activation, gene expression and post-translational protein modifications. This review is, thus, an attempt to summarize the new discoveries involving ROS and seed germination. The study of these interactions may supply markers of seed quality that might eventually be used in breeding programs to improve crop yields.

Proteomic analysis of seed germination under salt stress in soybeans

Soybean (Glycine max (L.) Merrill) is a salt-sensitive crop, and its production is severely affected by saline soils. Therefore, the response of soybean seeds to salt stress during germination was investigated at both physiological and proteomic levels. The salt-tolerant cultivar Lee68 and salt-sensitive cultivar N2899 were exposed to 100 mmol/L NaCl until radicle protrusion from the seed coat. In both cultivars, the final germination percentage was not affected by salt, but the mean germination times of Lee68 and N2899 were delayed by 0.3 and 1.0 d, respectively, compared with controls. In response to salt stress, the abscisic acid content increased, and gibberellic acid (GA₁+₃) and isopentenyladenosine decreased. Indole-3-acetic acid increased in Lee68, but remained unchanged in N2899. The proteins extracted from germinated seeds were separated using two-dimensional gel electrophoresis (2-DE), followed by Coomassie brilliant blue G-250 staining. About 350 protein spots from 2-DE gels of pH range 3 to 10 and 650 spots from gels of pH range 4 to 7 were reproducibly resolved, of which 18 protein spots showed changes in abundance as a result of salt stress in both cultivars. After matrix-assisted laser desorption ionization-time of flight-mass spectroscopy (MALDI-TOF-MS) analysis of the differentially expressed proteins, the peptide mass fingerprint was searched against the soybean UniGene database and nine proteins were successfully identified. Ferritin and 20S proteasome subunit β-6 were up-regulated in both cultivars. Glyceraldehyde 3-phosphate dehydrogenase, glutathione S-transferase (GST) 9, GST 10, and seed maturation protein PM36 were down-regulated in Lee68 by salt, but still remained at a certain level. However, these proteins were present in lower levels in control N2899 and were up-regulated under salt stress. The results indicate that these proteins might have important roles in defense mechanisms against salt stress during soybean seed germination.

cDNA cloning, characterization, and developmental expression of the 20S proteasome alpha5 subunit in the Mediterranean fruit fly Ceratitis capitata

In the present study, we report the cDNA cloning, characterization, and developmental expression of the 20S proteasome alpha5 subunit from the Mediterranean fruit fly Ceratitis capitata (medfly). Using an RT-PCR fragment that corresponds to the amino-terminal region of the Drosophila melanogaster 20S proteasome alpha5 subunit, we isolated a 987-bp cDNA that encodes the complete coding region of the medfly ortholog, which was named CcPSMA5. CcPSMA5 consists of 241 amino acids and has a predicted molecular weight of 26.4 kDa and pI 4.75. Comparison of the CcPSMA5 amino acid sequence with the sequences of all known 20S proteasome alpha5 subunits from different organisms indicated that the medfly 20S proteasome alpha5 subunit has the strongest homology to that of Drosophila. In situ hybridization showed that the CcPSMA5 gene is mapped in the region 44B of chromosome 4. Northern blot hybridization analysis showed that the CcPSMA5 mRNA has a size of approximately 1.2 kb. High levels of the CcPSMA5 mRNA were detected in freshly laid eggs, indicating that they were maternally deposited. The mRNA expression pattern during medfly development suggests that the CcPSMA5 gene is upregulated before mid-embryogenesis and at the onset of metamorphosis.

A proteomic approach in analyzing heat-responsive proteins in rice leaves

The present study investigated rice leaf proteome in response to heat stress. Rice seedlings were subjected to a temperature of 42 degrees C and samples were collected 12 and 24 h after treatment. Increased relative ion leakage and lipid peroxidation suggested that oxidative stress frequently was generated in rice leaves exposed to high temperature. 2-DE, coupled with MS, was used to investigate and identify heat-responsive proteins in rice leaves. In order to identify the low-abundant proteins in leaves, samples were prefractionated by 15% PEG. The PEG supernatant and the pellet fraction samples were separated by 2-DE, and visualized by silver or CBB staining. Approximately 1000 protein spots were reproducibly detected on each gel, wherein 73 protein spots were differentially expressed at least at one time point. Of these differentially expressed proteins, a total of 34 and 39 protein spots were found in the PEG supernatant and pellet fractions, respectively. Using MALDI-TOF MS, a total of 48 proteins were identified. These proteins were categorized into classes related to heat shock proteins, energy and metabolism, redox homeostasis, and regulatory proteins. The results of the present study show that a group of low molecular small heat shock proteins (sHSPs) were newly induced by heat stress. Among these sHSPs, a low molecular weight mitochondrial (Mt) sHSP was validated further by Western blot analysis. Furthermore, four differentially accumulated proteins that correspond to antioxidant enzymes were analyzed at the mRNA level, which confirmed the differential gene expression levels, and revealed that transcription levels were not completely concomitant with translation. The identification of some novel proteins in the heat stress response provides new insights that can lead to a better understanding of the molecular basis of heat-sensitivity in plants.

Proteome analysis of rice root proteins regulated by gibberellin

To gain an enhanced understanding of the mechanism by which gibberellins (GAs) regulate the growth and development of plants, it is necessary to identify proteins regulated by GA. Proteome analysis techniques have been applied as a direct, effective, and reliable tool in differential protein expressions. In previous studies, sixteen proteins showed differences in accumulation levels as a result of treatment with GA₃, uniconazole, or abscisic acid (ABA), and/or the differences between the GA-deficient semi-dwarf mutant, Tan-ginbozu, and normal cultivars. Among these proteins, aldolase increased in roots treated with GA₃, was present at low levels in Tan-ginbozu roots, and decreased in roots treated with uniconazole or ABA. In a root elongation assay, the growth of aldolase-antisense transgenic rice was half of that of vector control transgenic rice. These results indicate that increases in aldolase activity stimulate the glycolytic pathway and may play an important role in the GA-induced growth of roots. In this review, we discuss the relationship among GA, aldolase, and root growth.

Analysis of differentially expressed transcripts of fungal elicitor- and wound-treated wild rice (Oryza grandiglumis)

Suppression subtractive hybridization was used to construct a subtracted library (ogfw) from plants of a wild rice species, Oryza grandiglumis, subjected to a fungal elicitor and physical wounding. To screen the differentially expressed transcripts in the library, we applied a reverse Northern blot analysis to a cDNA microarray containing 1,152 random clones. Based on the average expression ratio, we selected 156 clones showing an elevated expression level. The elevated expression levels and overall expression profiles over time were verified by Northern blot analysis. A comparative functional categorization of the subtracted expressed sequence tags (ESTs) of the ogfw library against ESTs isolated from blast-infected O. sativa showed that the functional categories of cell rescue, defense and virulence, transcription, and cellular transport and transport mechanism of the ogfw library were threefold higher in the former than in the latter. These subtracted ESTs can be presumed to be related to the defense/resistance system and will be used to investigate the defense mechanisms of wild rice and to provide new insights into the genome of wild rice, which in turn will assist molecular breeding strategies of cultivated rice.

Technical aspects of functional proteomics in plants

Since the completion of genome sequences of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. This analysis is achieved by separation and identification of proteins, determination of their function and functional network, and construction of an appropriate database. Many improvements in separation and identification of proteins, such as two-dimensional electrophoresis, nano-liquid chromatography and mass spectrometry, have rapidly been achieved. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. These techniques have provided the possibility of high-throughput analysis of function and functional network of proteins in plants. However, to cope with the huge information emerging from proteome analyses, more sophisticated techniques and software are essential. The development and adaptation of such techniques will ease analyses of protein profiling, identification of post-translational modifications and protein-protein interaction, which are vital for elucidation of the protein functions.

Preferential induction of 20S proteasome subunits during elicitation of plant defense reactions: towards the characterization of "plant defense proteasomes"

Plants have evolved efficient mechanisms to resist pathogens. The earliest defense response is the hypersensitive response (HR) considered as the main step leading to plant systemic acquired resistance (SAR) that protects the whole plant against a large spectrum of pathogens. We showed previously that elicitation of defense reactions in tobacco cells by cryptogein, a proteinaceous elicitor of plant defense reactions, leads to a rapid and differential accumulation of transcripts corresponding to genes encoding defense-induced (din) subunits of 20S proteasome: beta1din, alpha3din and alpha6din.Here, expression of these three subunits was investigated by Northern blotting and by Western blotting using specific antibodies synthesized against two peptides deduced from the beta1din, alpha3din or alpha6din encoding sequence. Kinetics of mRNA and protein accumulation in various defense models showed a simultaneous accumulation of beta1din, alpha3din and alpha6din corresponding mRNAs and proteins only in plants developing a systemic acquired resistance. Inhibition by diphenyleneiodonium of the oxidative burst induced in defense reactions blocked the expression of beta1din, alpha3din and alpha6din. Using 2D gel electrophoresis and Western blotting, we showed multiple spots for each induced subunit suggesting the possible existence of multigenic families confirmed by genomic DNA analysis. These results suggest a complex regulation of induced subunits tightly correlated with the activation of plant defense reactions. beta1din, alpha3din and alpha6din subunits could probably replace the corresponding constitutive subunits in 20S proteasome leading to "plant defense proteasomes" which could play an important role in plant defense reactions.

The 20S proteasome

In contrast to our detailed knowledge of prokaryotic proteasomes, we have only a limited understanding of the prokaryotic regulators and their functional interaction with the proteasome. Most probably, we will soon learn more about the molecular structure and the mechanism of action of the prokaryotic regulators. Nevertheless, it still remains to be unravelled which signals or/and modifications transform an endogenous prokaryotic protein into a substrate of the proteasomal degradation machinery.

Metal resistance in yeast mediated by the expression of a maize 20S proteasome alpha subunit

Transformation of yeast cells with a maize cDNA ZmPAA, encoding a 20S proteasome alpha-subunit, conferred resistance to nickel, cadmium and cobalt. This resistance is not linked to a modification of the intracellular nickel content, as no accumulation of nickel was measured between yeast cells transformed with a void vector or the ZmPAA cDNA. The abundance of the ZmPAA mRNA was increased in the shoots of maize plants upon nickel treatment. These results suggest that the proteasome might be involved in nickel resistance by scavenging metal oxidized proteins both in plants and yeast.

Cryptogein affects expression of alpha3, alpha6 and beta1 20S proteasome subunits encoding genes in tobacco

Twelve alpha and beta 20S proteasome subunits cDNAs showing 70-82% identity with the corresponding genes in Arabidopsis or rice, and features of eukaryotic proteasome subunits were cloned in tobacco. Only beta1-tcI 7, alpha3 and alpha6, 20S proteasome subunits encoding genes were up-regulated by cryptogein, a proteinaceous elicitor of plant defence reactions. These results led to the hypothesis that the activation of beta1-tcI 7, alpha3 and alpha6 could induce a specific proteolysis involved in the hypersensitive response and systemic acquired resistance monitored by cryptogein.

OsPAA2, a distinct alpha 1 subunit gene for the 20S proteasome in rice (Oryza sativa L.)

The 20S proteasome is the proteolytic complex that is involved in removing abnormal proteins and other diverse biological functions. The 20S proteasome is constituted of 28 subunits arranged in four rings of seven subunits, and exists as a hollow cylinder. The two outer rings and the two inner rings are composed of seven different alpha and beta type subunits, respectively, giving an alpha 7 beta 7 beta 7 alpha 7 structure. We previously reported the primary structures of the 14 proteasomal subunit subfamilies in rice (Oryza sativa), representing the first set for all the subfamilies from monocot. In this study, a distinct cDNA sequence encoding the alpha1 subunit, OsPAA2, was identified. The amino acid sequence similarity between the two rice alpha1 subunits was as low as 59.6%, contrasting with those between paralogs of Arabidopsis proteasome subunit genes. The expression pattern of the OsPAA2 gene was different from that of another alpha1 gene, OsPAA1. These data suggest that OsPAA2 might play a distinct role from that of OsPAA1 in the 20S proteasome complex.