The serine carboxypeptidase like gene family of rice (Oryza sativa L. ssp. japonica)

Genome-Wide Analysis of the Serine Carboxypeptidase-like (SCPL) Protein Family of Bitter Gourd and Functional Validation of McSCPL22 in Fusarium oxysporum f. sp. Momordicae (FOM) Resistance

Bitter gourd is increasingly being recognized for its value as a vegetable and medicinal use, but the molecular mechanisms of pathogen resistance remain relatively poorly understood. The serine carboxypeptidase-like (SCPL) protein family plays a key role in plant growth, pathogen defense, and so on. However, a comprehensive identification and functional characterization of the SCPL gene family has yet to be conducted in bitter melon. In this study, 32 SCPL genes were identified in bitter gourd and divided into three classes. The number of SCPL genes contained in the three clusters was 7, 7, and 18, respectively. Most SCPL gene promoters contain cis-acting elements with light, hormone, and stress responses. The RNA sequencing data showed that the expression of several SCPL genes changed significantly after pathogen infection. In particular, expression of the McSCPL4, 10, 17, 22, and 25 genes increased substantially in the resistant varieties after infection, and their expression levels were higher than those in the susceptible varieties. These results suggested that genes such as McSCPL4, 10, 17, 22, and 25 may play a significant role in conferring resistance to fungal infections. Moreover, the expression levels of the McSCPL10, 17, 22, 23, and 25 genes were likewise significantly changed after being induced by salicylic acid (SA) and jasmonic acid (JA). In situ hybridization showed that McSCPL22 was expressed in the vascular tissues of infected plants, which largely overlapped with the location of Fusarium oxysporum f. sp. Momordicae (FOM) infection and the site of hydrogen peroxide production. Our results showed that McSCPL22 may be involved in the regulation of the SA and JA pathways and enhance resistance to FOM in bitter gourd plants. This is the first study to perform SCPL gene family analysis in bitter gourd. McSCPL22 may have the potential to enhance FOM resistance in bitter gourd, and further investigation into its function is warranted. The results of this study may enhance the yield and molecular breeding of bitter gourd.

Genome-Wide Analysis of Serine Carboxypeptidase-like Genes in Soybean and Their Roles in Stress Resistance

The serine carboxypeptidase-like (SCPL) gene family plays a crucial role in the regulation of plant growth, development, and stress response through activities such as acyltransferases in plant secondary metabolism pathways. Although SCPL genes have been identified in various plant species, their specific functions and characteristics in soybean (Glycine max) have not yet been studied. We identified and characterized 73 SCPL genes, grouped into three subgroups based on gene structure and phylogenetic relationships. These genes are distributed unevenly across 20 soybean chromosomes and show varied codon usage patterns influenced by both mutation and selection pressures. Gene ontology (GO) enrichment suggests these genes are involved in plant cell wall regulation and stress responses. Expression analysis in various tissues and under stress conditions, including the presence of numerous stress-related cis-acting elements, indicated that these genes have varied expression patterns. This suggests that they play specialized roles such as modulating plant defense mechanisms against nematode infections, enhancing tolerance to drought and high salinity, and responding to cold stress, thereby helping soybean adapt to environmental stresses. Moreover, the expression of specific GmSCPLs was significantly affected following exposure to nematode infection, drought, high salt (NaCl), and cold stresses. Our findings underscore the potential of SCPL genes in enhancing stress resistance in soybean, providing a valuable resource for future genetic improvement and breeding strategies.

Classification, biosynthesis, and biological functions of triterpene esters in plants

Triterpene esters comprise a class of secondary metabolites that are synthesized by decorating triterpene skeletons with a series of oxidation, glycosylation, and acylation modifications. Many triterpene esters with important bioactivities have been isolated and identified, including those with applications in the pesticide, pharmaceutical, and cosmetic industries. They also play essential roles in plant defense against pests, diseases, physical damage (as part of the cuticle), and regulation of root microorganisms. However, there has been no recent summary of the biosynthetic pathways and biological functions of plant triterpene esters. Here, we classify triterpene esters into five categories based on their skeletons and find that C-3 oxidation may have a significant effect on triterpenoid acylation. Fatty acid and aromatic moieties are common ligands present in triterpene esters. We further analyze triterpene ester synthesis-related acyltransferases (TEsACTs) in the triterpene biosynthetic pathway. Using an evolutionary classification of BAHD acyltransferases (BAHD-ATs) and serine carboxypeptidase-like acyltransferases (SCPL-ATs) in Arabidopsis thaliana and Oryza sativa, we classify 18 TEsACTs with identified functions from 11 species. All the triterpene-skeleton-related TEsACTs belong to BAHD-AT clades IIIa and I, and the only identified TEsACT from the SCPL-AT family belongs to the CP-I subfamily. This comprehensive review of the biosynthetic pathways and bioactivities of triterpene esters provides a foundation for further study of their bioactivities and applications in industry, agricultural production, and human health.

Genome-wide analysis of the serine carboxypeptidase-like protein family reveals Ga09G1039 is involved in fiber elongation in cotton

The Gossypium is a model genus for understanding polyploidy and the evolutionary pattern of inheritance. This study aimed to investigate the characteristics of SCPLs in different cotton species and their role in fiber development. A total of 891 genes from one typical monocot and ten dicot species were naturally divided into three classes based on phylogenetic analysis. The SCPL gene family in cotton has undergone intense purifying selection with some functional variation. Segmental duplication and whole genome duplication were shown to be the two main reasons for the increase in the number of genes during cotton evolution. The identification of Gh_SCPL genes exhibiting differential expression in particular tissues or response to environmental stimuli provides a new measure for the in-depth characterization of selected genes of importance. Ga09G1039 was involved in the developmental process of fibers and ovules, and it is significantly different from proteins from other cotton species in terms of phylogenetic, gene structure, conserved protein motifs and tertiary structure. Overexpression of Ga09G1039 significantly increased the length of stem trichomes. Ga09G1039 may be a serine carboxypeptidase protein with hydrolase activity, according to functional region, prokaryotic expression, and western blotting analysis. The results provide a comprehensive overview of the genetic basis of SCPLs in Gossypium and further our knowledge in understanding the key aspects of SCPLs in cotton with their potential role in fiber development and stress resistance.

Exploring Novel Polytubey Reproduction Pathways Utilizing Cumulative Genetic Tools

In the anthers and ovaries of flowers, pollen grains and embryo sacs are produced with uniform cell compositions. This stable gametogenesis enables elaborate interactions between male and female gametophytes after pollination, forming the highly successful sexual reproduction system in flowering plants. As most ovules are fertilized with a single pollen tube, the resulting genome set in the embryo and endosperm is determined in a single pattern by independent fertilization of the egg cell and central cell by two sperm cells. However, if ovules receive four sperm cells from two pollen tubes, the expected options for genome sets in the developing seeds would more than double. In wild-type Arabidopsis thaliana plants, around 5% of ovules receive two pollen tubes. Recent studies have elucidated the abnormal fertilization in supernumerary pollen tubes and sperm cells related to polytubey, polyspermy, heterofertilization and fertilization recovery. Analyses of model plants have begun to uncover the mechanisms underlying this new pollen tube biology. Here, we review unusual fertilization phenomena and propose several breeding applications for flowering plants. These arguments contribute to the remodeling of plant reproduction, a challenging concept that alters typical plant fertilization by utilizing the current genetic toolbox.

Melatonin: A promising candidate for maintaining food security under the threat of phytopathogens

Plant immune response is tightly controlled by an interplay of various phytohormones and plant growth regulators. Among them, the role of salicylic acid, jasmonic acid, and ethylene is well established while some others such as nitric oxide, polyamines, and hydrogen sulfide have appeared to be key regulators of plant immunity. In addition, some other chemicals, such as melatonin (N-acetyl-5-methoxytryptamine), are apparently turning out to be the novel regulators of plant defense responses. Melatonin has shown promising results in enhancing resistance of plants to a variety of pathogens including fungi, bacteria, and viruses, however, the molecular mechanism of melatonin-mediated plant immune regulation is currently elusive. Evidence gathered so far indicates that melatonin regulates plant immunity by (1) facilitating the maintenance of ROS homeostasis, (2) interacting with other phytohormones and growth regulators, and (3) inducing the accumulation of defense molecules. Therefore, engineering crops with improved melatonin production could enhance crop productivity under stress conditions. This review extends our understanding of the multifaceted role of melatonin in the regulation of plant defense response and presents a putative pathway of melatonin functioning and its interaction with phytohormones during biotic stress.

Leaf proteome reveals the alterations in photosynthesis and defense-related proteins between potato tetraploid cultivars and diploid wild species

Potato (Solanum tuberosum L.) as the important food crop worldwide has abundant morphological and genetic diversity. To understand the underlying molecular mechanisms determining phenotypic differences in wild species and cultivated potato, a comparative proteomics approach was applied to analyze leaf proteome alteration among three tetraploid cultivars and three diploid wild species using two-dimensional gel electrophoresis (2-DE). Quantitative image analysis showed a total of 47 protein spots with significantly altered abundance (>3-fold, P < 0.05), and 45 differentially abundant proteins were identified by MALDI-TOF/TOF MS. These proteins exhibited both the qualitative and quantitative changes. Most of them were involved in photosynthesis, cell defense and rescue, protein biosynthesis, which might exhibit the main differences between tetraploid cultivars and diploid wild species. The photosynthesis and protein biosynthesis-related proteins were up-regulated or only present in tetraploid cultivars, suggesting the higher photosynthetic efficiency and more newly synthesized peptides. It might contribute to some superior traits of tetraploid cultivars, such as larger leaf size, greater growth vigor, better tuber yield and quality. However, some cell defense and rescue-related proteins, especially the pathogenesis-related proteins and antioxidant enzymes, were up-regulated or only present in diploid wild species. It might be responsible for stronger resistance to diseases and pests or tolerance to environmental stresses in diploid wild species. This study would provide valuable information for the underlying molecular mechanisms of potato genetic diversity, and help in developing strategies for the utilization of wild species for potato improvement.

Genome-wide analysis of the serine carboxypeptidase-like (SCPL) proteins in Brassica napus L

The serine carboxypeptidase-like protein (SCPL) family plays a key part in plant growth, development and stress responses. However, the serine carboxypeptidase-like (SCPL) proteins in Brassica napus L. (B. napus) have not been reported yet. Here, we identified a total of 117 putative SCPL genes in B. napus, which were unevenly distributed on all 19 chromosomes and were divided into three groups (carboxypeptidase Ⅰ to Ⅲ) according to their phylogenetic relationships. Synteny and duplication analysis revealed that the SCPL gene family of B. napus was amplified during allopolyploidization, in which the whole genome triplication and dispersed duplication played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SCPL genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. Subsequently, the analyses of the gene structure, conserved motifs, cis-element and expression patterns showed that the members in the same group were highly conserved. Furthermore, candidate gene based association study suggested the role of BnSCPL52 in controlling seed number per silique, seed weight and silique length and a CAPS marker was developed to distinguish different haplotypes. Our results provide an overview of rapeseed SCPL genes that enable us for further functional research and benefit the marker-assisted breeding in Brassica napus.

The Serine Carboxypeptidase-Like Gene SCPL41 Negatively Regulates Membrane Lipid Metabolism in Arabidopsis thaliana

The Arabidopsis has 51 proteins annotated as serine carboxypeptidase-like (SCPL) enzymes. Although biochemical and cellular characterization indicates SCPLs involved in protein turnover or processing, little is known about their roles in plant metabolism. In this study, we identified an Arabidopsis mutant, bis4 (1-butanol insensitive 4), that was insensitive to the inhibitory effect of 1-butanol on seed germination. We cloned the gene that was defective in bis4 and found that it encoded an SCPL41 protein. Transgenic Arabidopsis plants constitutively expressing SCPL41 were generated, oil body staining and lipidomic assays indicated that SCPL41-overexpressing plants showed a decrease in membrane lipid content, especially digalactosyl diglyceride (DGDG) and monogalactosyl diglyceride (MGDG) contents, while the loss of SCPL41 increased the membrane lipid levels compared with those in wild-type plants. These findings suggested that SCPL41 had acquired novel functions in membrane lipid metabolism.

Molecular host mimicry and manipulation in bacterial symbionts

It is common among intracellular bacterial pathogens to use eukaryotic-like proteins that mimic and manipulate host cellular processes to promote colonization and intracellular survival. Eukaryotic-like proteins are bacterial proteins with domains that are rare in bacteria, and known to function in the context of a eukaryotic cell. Such proteins can originate through horizontal gene transfer from eukaryotes or, in the case of simple repeat proteins, through convergent evolution. Recent studies of microbiomes associated with several eukaryotic hosts suggest that similar molecular strategies are deployed by cooperative bacteria that interact closely with eukaryotic cells. Some mimics, like ankyrin repeats, leucine rich repeats and tetratricopeptide repeats are shared across diverse symbiotic systems ranging from amoebae to plants, and may have originated early, or evolved independently in multiple systems. Others, like plant-mimicking domains in members of the plant microbiome are likely to be more recent innovations resulting from horizontal gene transfer from the host, or from microbial eukaryotes occupying the same host. Host protein mimics have only been described in a limited set of symbiotic systems, but are likely to be more widespread. Systematic searches for eukaryote-like proteins in symbiont genomes could lead to the discovery of novel mechanisms underlying host-symbiont interactions.

A quantitative proteomic analysis of the molecular mechanism underlying fertility conversion in thermo-sensitive genetic male sterility line AnnongS-1

BACKGROUND

Thermo-sensitive genetic male sterile (TGMS) lines have been widely used in two-line hybrid rice breeding. The two-line hybrids have increased rice yields substantially. However, the effect of environmental temperatures on the fertility conversion is still not fully clear. In this study, we performed a tandem mass tag (TMT)-based proteomic analysis on the anthers of the TGMS line AnnongS-1 grown under permissive (low) temperature (21 °C) and restrictive (high) temperature (> 26 °C) conditions in an attempt to explore the effect of temperature on the fertility of the male sterile line.

RESULTS

After the AnnongS-1 plants were induced under either permissive or restrictive conditions, morphological observations and I₂-KI staining confirmed that the pollen grains formed under high temperature conditions were abortive while those formed under low temperature developed normally. In comparison to the plants grown under permissive conditions, the restrictive high-temperature conditions led to the differential accumulation of 89 proteins in the anthers, of which 46 were increased in abundance and 43 were decreased in abundance. Most of the subcellular compartments of the anther cells had one or more proteins that had been differentially accumulated, with the cytoplasm and chloroplast having the greatest accumulations. More than 40% of the differentially abundant proteins (DAPs) were enzymes involved in photosynthesis, energy metabolism, biosynthesis and catabolism of cellular components, metabolic regulation, defense and stress, etc. The DAPs related to protein metabolism accounted for the largest proportion (21.35%), followed by those related to defense and stress (12.36%), metabolic regulation (10.11%) and carbohydrate metabolism (8.99%), indicating that such biological processes in anther cells were more susceptible to high temperature stress.

CONCLUSIONS

The restrictive temperature induction caused fertility-sterility conversion in the TGMS line AnnongS-1 mainly by adversely affecting the metabolism of protein, carbohydrate and energy, and decreasing the abundances of important proteins closely related to defense and stress, thereby impeding the growth and development of the pollen and weakening the overall defense and ability to endure stress of AnnongS-1. These data are helpful for deepening our understanding of the molecular mechanism underlying fertility conversion in TGMS lines.

Characterization of a strong and constitutive promoter from the Arabidopsis serine carboxypeptidase-like gene AtSCPL30 as a potential tool for crop transgenic breeding

BACKGROUND

Transgenic technology has become an important technique for crop genetic improvement. The application of well-characterized promoters is essential for developing a vector system for efficient genetic transformation. Therefore, isolation and functional validation of more alternative constitutive promoters to the CaMV35S promoter is highly desirable.

RESULTS

In this study, a 2093-bp sequence upstream of the translation initiation codon ATG of AtSCPL30 was isolated as the full-length promoter (PD1). To characterize the AtSCPL30 promoter (PD1) and eight 5' deleted fragments (PD2-PD9) of different lengths were fused with GUS to produce the promoter::GUS plasmids and were translocated into Nicotiana benthamiana. PD1-PD9 could confer strong and constitutive expression of transgenes in almost all tissues and development stages in Nicotiana benthamiana transgenic plants. Additionally, PD2-PD7 drove transgene expression consistently over twofold higher than the well-used CaMV35S promoter under normal and stress conditions. Among them, PD7 was only 456 bp in length, and its transcriptional activity was comparable to that of PD2-PD6. Moreover, GUS transient assay in the leaves of Nicotiana benthamiana revealed that the 162-bp (- 456~ - 295 bp) and 111-bp (- 294~ - 184 bp) fragments from the AtSCPL30 promoter could increase the transcriptional activity of mini35S up to 16- and 18-fold, respectively.

CONCLUSIONS

As a small constitutive strong promoter of plant origin, PD7 has the advantage of biosafety and reduces the probability of transgene silencing compared to the virus-derived CaMV35S promoter. PD7 would also be an alternative constitutive promoter to the CaMV35S promoter when multigene transformation was performed in the same vector, thereby avoiding the overuse of the CaMV35S promoter and allowing for the successful application of transgenic technology. And, the 162- and 111-bp fragments will also be very useful for synthetic promoter design based on their high enhancer activities.

Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herb Persicaria minor leaves upon methyl jasmonate elicitation

BACKGROUND

Jasmonic acid (JA) and its derivative, methyl JA (MeJA) are hormonal cues released by plants that signal defense response to curb damages from biotic and abiotic stresses. To study such response, a tropical herbal plant, Persicaria minor, which possesses pungent smell and various bioactivities including antimicrobial and anticancer, was treated with MeJA. Such elicitation has been performed in hairy root cultures and plants such as Arabidopsis and rice, yet how MeJA influenced the proteome of an herbal species like P. minor is unknown.

METHOD

In this study, P. minor plants were exogenously elicited with MeJA and leaf samples were subjected to SWATH-MS proteomics analysis. A previously published translated transcriptome database was used as a reference proteome database for a comprehensive protein sequence catalogue and to compare their differential expression.

RESULTS

From this proteomics informed by transcriptomics approach, we have successfully profiled 751 proteins of which 40 proteins were significantly different between control and MeJA-treated samples. Furthermore, a correlation analysis between both proteome and the transcriptome data sets suggests that significantly upregulated proteins were positively correlated with their cognate transcripts (Pearson's r = 0.677) while a weak correlation was observed for downregulated proteins (r = 0.147).

DISCUSSION

MeJA treatment induced the upregulation of proteins involved in various biochemical pathways including stress response mechanism, lipid metabolism, secondary metabolite production, DNA degradation and cell wall degradation. Conversely, proteins involved in energy expensive reactions such as photosynthesis, protein synthesis and structure were significantly downregulated upon MeJA elicitation. Overall protein-transcript correlation was also weak (r = 0.341) suggesting the existence of post-transcriptional regulation during such stress. In conclusion, proteomics analysis using SWATH-MS analysis supplemented by the transcriptome database allows comprehensive protein profiling of this non-model herbal species upon MeJA treatment.

A serine carboxypeptidase-like acyltransferase catalyzes synthesis of indole-3-acetic (IAA) ester conjugate in rice (Oryza sativa)

Indole-3-acetic acid (IAA) conjugation is one of mechanisms responsible for regulation of free auxin levels in plants. A new member of the serine carboxypeptidase-like (SCPL) acyltransferases family from Oryza sativa has been cloned and characterized. 1-O-indole-3-acetyl-β-D-glucose (1-O-IAGlc): myo-inositol acyltransferase (IAInos synthase) is an enzyme of IAA ester conjugates biosynthesis pathway that catalyzes transfer of IAA moiety from 1-O-IAGlc to myo-inositol forming IA-myo-inositol (IAInos). The OsIAA-At cDNA has been cloned and expressed using yeast and bacterial expression systems. Proteins produced in Saccharomyces cerevisiae and Escherichia coli contained 483 and 517 amino acids, respectively. The enzyme functionally expressed in both expression systems exhibits 1-O-IAGlc-dependent acyltransferase activity. Analysis of amino acid sequence confirmed that rice IAInos synthase belongs to the SCPL protein family. Recombinant IAInos synthases produced in yeast and bacterial expression systems have been partially characterized and their properties have been compared to those of the native enzyme obtained from 6-days-old rice seedlings by biochemical approach. The oligosaccharide component of the protein enzyme is not necessary for its catalytic activity. The native enzyme showed the lowest specific activity of 5.01 nmol min^-1 mg^-1 protein, whereas the recombinant enzymes produced in yeast and bacteria showed specific activity of 18.75 nmol min^-1 mg^-1 protein and 18.09 nmol min^-1 mg^-1 protein, respectively. The K_M values for myo-inositol were similar for all three forms of the enzyme: 1.38, 0.83, 1.0 mM for native, bacterial and yeast protein, respectively. Both recombinant forms of IAInos synthase and the native enzyme also have the same optimal pH of 7.4 and all of them are inhibited by phenylmethylsulfonyl fluoride (PMSF), specific inhibitor of serine carboxypeptidases.

Genome-wide identification, classification and expression analysis of the serine carboxypeptidase-like protein family in poplar

Previous studies have shown that the serine carboxypeptidase-like (SCPL) proteins in several plants play a key part in plant growth, development and stress responses. However, little is known about the functions of the SCPL genes in poplar. We identified 57 SCPL genes and divided into 3 subfamilies, which were unevenly distributed on 19 poplar chromosomes. Gene structure indicated that SCPL genes contain more introns, and motifs of each subfamily were relatively conserved. There were a total of 14 pairs of paralogs, with 6 pairs of these paralogs generated by segmental duplication and 1 generated by tandem duplication. In microsynteny analysis, large-scale duplication events played a key part in the expansion of Carboxypeptidase III genes. Expression of these genes was higher in mature leaf. Quantitative real-time PCR showed that majority of the SCPL genes were induced by methyl jasmonate (MeJA) treatment. PtSCPL27 and PtSCPL40 were located on the cytomembrane by conducting subcellular localization analysis. Our paper provides a theoretical basis for further functional research of PtSCPL genes and will benefit the molecular breeding for resistance to disease in poplar.

Comparative proteomics reveals that central metabolism changes are associated with resistance against Sporisorium scitamineum in sugarcane

BACKGROUND

Sugarcane smut, which is caused by Sporisorium scitamineum, has been threatening global sugarcane production. Breeding smut resistant sugarcane varieties has been proven to be the most effective method of controlling this particular disease. However, a lack of genome information of sugarcane has hindered the development of genome-assisted resistance breeding programs. Furthermore, the molecular basis of sugarcane response to S. scitamineum infection at the proteome level was incomplete and combining proteomic and transcriptional analysis has not yet been conducted.

RESULTS

We identified 273 and 341 differentially expressed proteins in sugarcane smut-resistant (Yacheng05-179) and susceptible (ROC22) genotypes at 48 h after inoculation with S. scitamineum by employing an isobaric tag for relative and absolute quantification (iTRAQ). The proteome quantitative data were then validated by multiple reaction monitoring (MRM). The integrative analysis showed that the correlations between the quantitative proteins and the corresponding genes that was obtained in our previous transcriptome study were poor, which were 0.1502 and 0.2466 in Yacheng05-179 and ROC22, respectively, thereby revealing a post-transcriptional event during Yacheng05-179-S. scitamineum incompatible interaction and ROC22-S. scitamineum compatible interaction. Most differentially expressed proteins were closely related to sugarcane smut resistance such as beta-1,3-glucanase, peroxidase, pathogenesis-related protein 1 (PR1), endo-1,4-beta-xylanase, heat shock protein, and lectin. Ethylene and gibberellic acid pathways, phenylpropanoid metabolism and PRs, such as PR1, PR2, PR5 and PR14, were more active in Yacheng05-179, which suggested of their possible roles in sugarcane smut resistance. However, calcium signaling, reactive oxygen species, nitric oxide, and abscisic acid pathways in Yacheng05-179 were repressed by S. scitamineum and might not be crucial for defense against this particular pathogen.

CONCLUSIONS

These results indicated complex resistance-related events in sugarcane-S. scitamineum interaction, and provided novel insights into the molecular mechanism underlying the response of sugarcane to S. scitamineum infection.

Serine carboxypeptidase 46 Regulates Grain Filling and Seed Germination in Rice (Oryza sativa L.)

Serine carboxypeptidase (SCP) is one of the largest groups of enzymes catalyzing proteolysis for functional protein maturation. To date, little is known about the function of SCPs in rice. In this study, we present a comprehensive analysis of the gene structure and expression profile of 59 rice SCPs. SCP46 is dominantly expressed in developing seeds, particularly in embryo, endosperm and aleurone layers, and could be induced by ABA. Functional characterization revealed that knock-down of SCP46 resulted in smaller grain size and enhanced seed germination. Furthermore, scp46 seed germination became less sensitive to the ABA inhibition than the Wild-type did; suggesting SCP46 is involved in ABA signaling. As indicated by RNA-seq and qRT-PCR analysis, numerous grain filling and seed dormancy related genes, such as SP, VP1 and AGPs were down-regulated in scp46. Yeast-two-hybrid assay also showed that SCP46 interacts with another ABA-inducible protein DI19-1. Taken together, we suggested that SCP46 is a master regulator of grain filling and seed germination, possibly via participating in the ABA signaling. The results of this study shed novel light into the roles of SCPs in rice.

Differential expression of GS5 regulates grain size in rice

Grain weight is a major determinant of grain yield. GS5 is a positive regulator of grain size such that grain width, filling, and weight are correlated with its expression level. Previous work suggested that polymorphisms of GS5 in the promoter region might be responsible for the variation in grain size. In this study, two single nucleotide polymorphisms (SNPs) between the wide-grain allele GS5-1 and the narrow-grain allele GS5-2 in the upstream region of the gene that were responsible for the differential expression in developing young panicles were identified. These two polymorphs altered the responses of the GS5 alleles to abscisic acid (ABA) treatments, resulting in higher expression of GS5-1 than of GS5-2 in developing young panicles. It was also shown that SNPs in light-responsive elements of the promoter altered the response to light induction, leading to higher expression of GS5-2 than GS5-1 in leaves. Enhanced expression of GS5 competitively inhibits the interaction between OsBAK1-7 and OsMSBP1 by occupying the extracellular leucine-rich repeat (LRR) domain of OsBAK1-7, thus preventing OsBAK1-7 from endocytosis caused by interacting with OsMSBP1, providing an explanation for the positive association between grain size and GS5 expression. These results advanced our understanding of the molecular mechanism by which GS5 controls grain size.

Characterization of the largest effector gene cluster of Ustilago maydis

In the genome of the biotrophic plant pathogen Ustilago maydis, many of the genes coding for secreted protein effectors modulating virulence are arranged in gene clusters. The vast majority of these genes encode novel proteins whose expression is coupled to plant colonization. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. Here we present the functional analysis of this genomic region. We show that a 19A deletion mutant behaves like an endophyte, i.e. is still able to colonize plants and complete the infection cycle. However, tumors, the most conspicuous symptoms of maize smut disease, are only rarely formed and fungal biomass in infected tissue is significantly reduced. The generation and analysis of strains carrying sub-deletions identified several genes significantly contributing to tumor formation after seedling infection. Another of the effectors could be linked specifically to anthocyanin induction in the infected tissue. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. We propose that the analysis of plant responses to effector mutant strains that lack a strong virulence phenotype may be a general way to visualize differences in effector function.

Natural variation and artificial selection in four genes determine grain shape in rice

The size of cultivated rice (Oryza sativa) grains has been altered by both domestication and artificial selection over the course of evolutionary history. Several quantitative trait loci (QTLs) for grain size have been cloned in the past 10 yr. To explore the natural variation in these QTLs, resequencing of grain width and weight 2 (GW2), grain size 5 (GS5) and QTL for seed width 5 (qSW5) and genotyping of grain size 3 (GS3) were performed in the germplasms of 127 varieties of rice (O. sativa) and 10-15 samples of wild rice (Oryza rufipogon). Ten, 10 and 15 haplotypes were observed for GW2, GS5 and qSW5. qSW5 and GS3 had the strongest effects on grain size, which have been widely utilized in rice production, whereas GW2 and GS5 showed more modest effects. GS5 showed small sequence variations in O. sativa germplasm and that of its progenitor O. rufipogon. qSW5 exhibited the highest level of nucleotide diversity. GW2 showed signs of purifying selection. The four grain size genes experienced different selection intensities depending on their genetic effects. In the indica population, linkage disequilibrium (LD) was detected among GS3, qSW5 and GS5. The substantial genetic variation in these four genes provides the flexibility needed to design various rice grain shapes. These findings provide insight into the evolutionary features of grain size genes in rice.

Genome expression profile analysis of the immature maize embryo during dedifferentiation

Maize is one of the most important cereal crops worldwide and one of the primary targets of genetic manipulation, which provides an excellent way to promote its production. However, the obvious difference of the dedifferentiation frequency of immature maize embryo among various genotypes indicates that its genetic transformation is dependence on genotype and immature embryo-derived undifferentiated cells. To identify important genes and metabolic pathways involved in forming of embryo-derived embryonic calli, in this study, DGE (differential gene expression) analysis was performed on stages I, II, and III of maize inbred line 18-599R and corresponding control during the process of immature embryo dedifferentiation. A total of ∼21 million cDNA tags were sequenced, and 4,849,453, 5,076,030, 4,931,339, and 5,130,573 clean tags were obtained in the libraries of the samples and the control, respectively. In comparison with the control, 251, 324 and 313 differentially expressed genes (DEGs) were identified in the three stages with more than five folds, respectively. Interestingly, it is revealed that all the DEGs are related to metabolism, cellular process, and signaling and information storage and processing functions. Particularly, the genes involved in amino acid and carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis and signal transduction mechanism have been significantly changed during the dedifferentiation. To our best knowledge, this study is the first genome-wide effort to investigate the transcriptional changes in dedifferentiation immature maize embryos and the identified DEGs can serve as a basis for further functional characterization.

NtSCP1 from tobacco is an extracellular serine carboxypeptidase III that has an impact on cell elongation

The leaf extracellular space contains several peptidases, most of which are of unknown function. We isolated cDNAs for two extracellular serine carboxypeptidase III genes from tobacco (Nicotiana tabacum), NtSCP1 and NtSCP2, belonging to a phylogenetic clade not yet functionally characterized in plants. NtSCP1 and NtSCP2 are orthologs derived from the two ancestors of tobacco. Reverse transcription-polymerase chain reaction analysis showed that NtSCP1 and NtSCP2 are expressed in root, stem, leaf, and flower tissues. Expression analysis of the β-glucuronidase reporter gene fused to the NtSCP1 transcription promoter region confirmed this expression profile. Western blotting of NtSCP1 and expression of an NtSCP1-green fluorescent protein fusion protein showed that the protein is located in the extracellular space of tobacco leaves and culture cells. Purified His-tagged NtSCP1 had carboxypeptidase activity in vitro. Transgenic tobacco plants overexpressing NtSCP1 showed a reduced flower length due to a decrease in cell size. Etiolated seedlings of these transgenic plants had shorter hypocotyls. These data provide support for a role of an extracellular type III carboxypeptidase in the control of cell elongation.

Proteomic analysis of a sea-ice diatom: salinity acclimation provides new insight into the dimethylsulfoniopropionate production pathway

Dimethylsulfoniopropionate (DMSP) plays important roles in oceanic carbon and sulfur cycling and may significantly impact climate. It is a biomolecule synthesized from the methionine (Met) pathway and proposed to serve various physiological functions to aid in environmental stress adaptation through its compatible solute, cryoprotectant, and antioxidant properties. Yet, the enzymes and mechanisms regulating DMSP production are poorly understood. This study utilized a proteomics approach to investigate protein changes associated with salinity-induced DMSP increases in the model sea-ice diatom Fragilariopsis cylindrus (CCMP 1102). We hypothesized proteins associated with the Met-DMSP biosynthesis pathway would increase in relative abundance when challenged with elevated salinity. To test this hypothesis axenic log-phase cultures initially grown at a salinity of 35 were gradually shifted to a final salinity of 70 over a 24-h period. Intracellular DMSP was measured and two-dimensional gel electrophoresis was used to identify protein changes at 48 h after the shift. Intracellular DMSP increased by approximately 85% in the hypersaline cultures. One-third of the proteins increased under high salinity were associated with amino acid pathways. Three protein isoforms of S-adenosylhomo-cysteine hydrolase, which synthesizes a Met precursor, increased 1.8- to 2.1-fold, two isoforms of S-adenosyl Met synthetase increased 1.9- to 2.5-fold, and S-adenosyl Met methyltransferase increased by 2.8-fold, suggesting active methyl cycle proteins are recruited in the synthesis of DMSP. Proteins from the four enzyme classes of the proposed algal Met transaminase DMSP pathway were among the elevated proteins, supporting our hypothesis and providing candidate genes for future characterization studies.

Plant protein-coding gene families: emerging bioinformatics approaches

Protein-coding gene families are sets of similar genes with a shared evolutionary origin and, generally, with similar biological functions. In plants, the size and role of gene families has been only partially addressed. However, suitable bioinformatics tools are being developed to cluster the enormous number of sequences currently available in databases. Specifically, comparative genomic databases promise to become powerful tools for gene family annotation in plant clades. In this review, I evaluate the data retrieved from various gene family databases, the ease with which they can be extracted and how useful the extracted information is.

Functional Characterization of a Putative Serine Carboxypeptidase in Vascular Smooth Muscle Cells

Rationale: We previously identified a novel serine carboxypeptidase, SCPEP1, that undergoes cleavage across all tissues where it is expressed. SCPEP1 bears the signature catalytic triad found in all serine carboxypeptidases, but its biological function is completely unknown.

Objective: To begin elucidating the functions of SCPEP1 in vitro and in the vessel wall after injury.

Methods and Results: Cultured smooth muscle cells were transduced with adenovirus carrying wild-type Scpep1 , a short hairpin RNA to Scpep1 , or variants of Scpep1 with mutations that disrupt the catalytic triad domain or SCPEP1 cleavage. Western blotting of key growth regulators or growth and migratory responses were assessed following SCPEP1 gain- or loss-of-function in smooth muscle cells. Vascular injury-induced remodeling and cell proliferation were evaluated in wild-type or newly created Scpep1 knockout mice. Overexpression of wild-type or cleavage-defective SCPEP1, but not a catalytic triad mutant SCPEP1, promotes smooth muscle cell proliferation and migration in vitro. A short hairpin RNA to Scpep1 blunts endogenous growth, which is rescued on concurrent expression of Scpep1 carrying silent mutations that evade knockdown. SCPEP1 protein is highly expressed in the neointima of 2 models of vascular remodeling. Scpep1 -null mice show decreases in medial and intimal cell proliferation as well as vessel remodeling following arterial injury.

Conclusions: SCPEP1 promotes smooth muscle cell proliferation and migration in a catalytic triad-dependent, cleavage-independent manner. SCPEP1 represents a new mediator of vascular remodeling and a potential therapeutic target for the treatment of vascular occlusive diseases.

Purification and subcellular localization of a secreted 75 kDa Trypanosoma cruzi serine oligopeptidase

An extracellular serine peptidase was purified 460-fold from Trypanosoma cruzi epimastigotes culture supernatant with (NH(4))(2)SO(4) precipitation followed by affinity chromatography aprotinin-agarose and continuous elution electrophoresis, yielding a total recovery of 65%. The molecular mass of the active enzyme estimated by reducing and non-reducing SDS-PAGE was about 75kDa. The optimal pH and temperature of this glycosylated peptidase were 8.0 and 37 degrees C using alpha-N-rho-tosyl-L-arginine-methyl ester (L-TAME) as substrate. The enzyme did not hydrolyze polypeptide substrates but was active against short peptide substrates containing arginine at the P1 site, in both ester and amide bonds. The peptidase was inhibited by TPCK and TCLK but not by other protease inhibitors suggesting that the enzyme belongs to the serine peptidase class. Interestingly, the enzyme seems to demonstrate some metal dependence since its activity was reduced by 1,10-phenanthroline, calcium and zinc ions. Rabbit anti-T. cruzi extracellular serine peptidase antiserum was used to show that the enzyme was restricted to intracellular structures, including the flagellar pocket, plasma membrane and cytoplasmic vesicles resembling reservosomes. These results suggest that the serine oligopeptidase is secreted into the extracellular environment through the flagellar pocket and the intracellular location could suggest its participation in certain proteolysis events in reservosomes. These findings show that this peptidase is a novel T. cruzi serine oligopeptidase, which differs not only from other peptidases described in the same parasite but also in other species of Trypanosoma.

A rice serine carboxypeptidase-like gene OsBISCPL1 is involved in regulation of defense responses against biotic and oxidative stress

Serine carboxypeptidase-like proteins (SCPLs) comprise a large family of protein hydrolyzing enzymes that play roles in multiple cellular processes. During the course of study aimed at elucidating the molecular basis of induced immunity in rice, a gene, OsBISCPL1, encoding a putative SCPL, was isolated and identified. OsBISCPL1 contains a conserved peptidase S10 domain, serine active site and a signal peptide at N-terminus. OsBISCPL1 is expressed ubiquitously in rice, including roots, stems, leaves and spikes. Expression of OsBISCPL1 in leaves was significantly up-regulated after treatments with benzothiadiazole, salicylic acid, jasmonic acid and 1-amino cyclopropane-1-carboxylic acid, and also up-regulated in incompatible interactions between rice and the blast fungus, Magnaporthe grisea. Transgenic Arabidopsis plants with constitutive expression of OsBISCPL1 were generated and disease resistance assays indicated that the OsBISCPL1-overexpressing plants showed an enhanced disease resistance against Pseudomonas syringae pv. tomato and Alternaria brassicicola. Expression levels of defense-related genes, e.g. PR1, PR2, PR5 and PDF1.2, were constitutively up-regulated in transgenic plants as compared with those in wild-type plants. Furthermore, the OsBISCPL1-overexpressing plants also showed an increased tolerance to oxidative stress and up-regulated expression of oxidative stress-related genes. The results suggest that the OsBISCPL1 may be involved in regulation of defense responses against pathogen infection and oxidative stress.

Identification of early senescence-associated genes in rice flag leaves

Leaf senescence is one of the key stages of plant leaf development. It is a highly complex but ordered process involving expression of large scale senescence associated genes, and its molecular mechanisms still remain unclear. By using suppression subtractive hybridization, 815 ESTs that are up-regulated at the onset of rice flag leaf senescence have been isolated. A total of 533 unigenes have been confirmed by macroarray detection and sequencing. 183 of these unigenes have GO annotations, involved in macromolecule metabolism, protein biosynthesis regulation, energy metabolism, gene expression regulations, detoxification, pathogenicity and stress, cytoskeleton organization and flower development. Another 121 unigenes co-localized with previously reported known stay-green QTLS. RT-PCR analysis on the other novel genes indicated that they can be up-regulated in natural early senescence and induced by hormone. Our results indicate that senescence is closely related to various metabolic pathways, thus providing new insight into the onset of leaf senescence mechanism.

Tissue expression of the novel serine carboxypeptidase Scpep1

We previously identified a novel gene designated retinoid-inducible serine carboxypeptidase (RISC or Scpep1). Here we characterize a polyclonal antibody raised to Scpep1 and assess its localization in mouse cells and tissues. Western blot analysis revealed an immunospecific approximately 35-kDa protein corresponding to endogenous Scpep1. This protein is smaller than the predicted approximately 51-kDa, suggesting that Scpep1 is proteolytically cleaved to a mature enzyme. Immunohistochemical studies demonstrate Scpep1 expression in embryonic heart and vasculature as well as in adult aortic smooth muscle cells and endothelial cells. Scpep1 displays a broad expression pattern in adult tissues with detectable levels in epithelia of digestive tract and urinary bladder, islet of Langerhans, type II alveolar cells and macrophages of lung, macrophage-like cells of lymph nodes and spleen, Leydig cells of testis, and nerve fibers in brain and ganglia. Consistent with previous mRNA studies in kidney, Scpep1 protein is restricted to proximal convoluted tubular epithelium (PCT). Immunoelectron microscopy shows enriched Scpep1 within lysosomes of the PCT, and immunofluorescence microscopy colocalizes Scpep1 with lysosomal-associated membrane protein-2. These results suggest that Scpep1 is a widely distributed lysosomal protease requiring proteolytic cleavage for activity. The highly specific Scpep1 antibody characterized herein provides a necessary reagent for elucidating Scpep1 function.

Expression genetics and haplotype analysis reveal cis regulation of serine carboxypeptidase I (Cxp1), a candidate gene for malting quality in barley (Hordeum vulgare L.)

Using a cDNA array-based functional genomics approach in barley, several candidate genes for malting quality including serine carboxypeptidase I (Cxp1) were previously identified (Potokina et al. in Mol Breed 14:153, 2004). The gene was mapped as a single nucleotide polymorphism (SNP) marker on chromosome 3H using the Steptoe (feeding grade)xMorex (malting grade) mapping population. Subsequently, the relative level of Cxp1 expression was determined by real-time RT-PCR for each of the 134 progeny lines and mapped as a quantitative trait. Only one quantitative trait locus (QTL) could be identified that significantly influenced the level of the Cxp1 expression. The expressed QTL maps to the same region on chromosome 3H as does the structural gene and corresponds to a QTL for "diastatic power," one among several traits measured to assess malting quality. An analysis of 90 barley cultivars sampled from a worldwide collection revealed six SNPs at the Cxp1 locus, three of which display complete linkage disequilibrium and define two haplotypes. The Cxp1 expression level in a set of barley accessions showing haplotype I was significantly higher than that of accessions displaying haplotype II. The data provide evidence that (1) the expression of Cxp1 is regulated in cis and that (2) the level of diastatic power in the barley seed is influenced by the level of Cxp1 expression.