Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies

Genome-wide analysis revealed the stepwise origin and functional diversification of HSDs from lower to higher plant species

Hydroxysteroid dehydrogenase (HSDs) is an oil-body sterol protein (steroleosin) with an NADP(H) binding domain that belongs to the short-chain dehydrogenase/reductase (SDR) superfamily. There are numerous studies on the characterization of HSDs in plants. However, thus far, the evolutionary differentiation and divergence analysis of these genes remain to be explored. The current study used an integrated method to elucidate the sequential evolution of HSDs in 64 sequenced plant genomes. Analyses were conducted on their origins, distribution, duplication, evolutionary paths, domain functions, motif composition, properties, and cis-elements. Results indicate that except for algae, HSD1 was widely distributed in plant species ranging from lower to higher plants, while HSD5 was restricted to terrestrial plants, and HSD2 was identified in fewer monocots and several dicot plants. Phylogenetic analysis of HSD proteins revealed that monocotyledonous HSD1 in moss and ferns appeared closest to the outgroup, V. carteri HSD-like, M. musculus HSD1, and H. sapiens HSD1. These data support the hypothesis that HSD1 originated in bryophytes and then in non-vascular and vascular plants, followed by HSD5 only in land plants. Gene structure analysis suggests that HSDs in plant species came up with a fixed number of six exons, and the intron phase was primarily 0, 1, 0, 0, and 0. Similarly, duplication analysis revealed that segmental duplications were the main reason for HSDs in plant species. Physicochemical properties suggest that dicotyledonous HSD1s and HSD5s were mainly acidic. The monocotyledonous HSD1s and HSD2s and the dicotyledonous HSD2s, HSD3s, HSD4s, and HSD6s were mainly basic, implying that HSDs in plants may have a variety of functions. Cis-regulatory elements and expression analysis revealed that HSDs in plants might have roles in several abiotic stresses. Due to the high expression of HSD1s and HSD5s in seeds, these HSDs in plants may have roles in fatty acid accumulation and degradation.

Caleosin/peroxygenases: multifunctional proteins in plants

BACKGROUND

Caleosin/peroxygenases (CLO/PXGs) are a family of multifunctional proteins that are ubiquitous in land plants and are also found in some fungi and green algae. CLO/PXGs were initially described as a class of plant lipid-associated proteins with some similarities to the oleosins that stabilize lipid droplets (LDs) in storage tissues, such as seeds. However, we now know that CLO/PXGs have more complex structures, distributions and functions than oleosins. Structurally, CLO/PXGs share conserved domains that confer specific biochemical features, and they have diverse localizations and functions.

SCOPE

This review surveys the structural properties of CLO/PXGs and their biochemical roles. In addition to their highly conserved structures, CLO/PXGs have peroxygenase activities and are involved in several aspects of oxylipin metabolism in plants. The enzymatic activities and the spatiotemporal expression of CLO/PXGs are described and linked with their wider involvement in plant physiology. Plant CLO/PXGs have many roles in both biotic and abiotic stress responses in plants and in their responses to environmental toxins. Finally, some intriguing developments in the biotechnological uses of CLO/PXGs are addressed.

CONCLUSIONS

It is now two decades since CLO/PXGs were first recognized as a new class of lipid-associated proteins and only 15 years since their additional enzymatic functions as a new class of peroxygenases were discovered. There are many interesting research questions that remain to be addressed in future physiological studies of plant CLO/PXGs and in their recently discovered roles in the sequestration and, possibly, detoxification of a wide variety of lipidic xenobiotics that can challenge plant welfare.

A computational study on the structure-function relationships of plant caleosins

Plant cells store energy in oil bodies constructed by structural proteins such as oleosins and caleosins. Although oil bodies usually accumulate in the seed and pollen of plants, caleosins are present in various organs and organelles. This issue, coupled with the diverse activities of caleosins, complicates the description of these oleo-proteins. Therefore, the current article proposes a new classification based on the bioinformatics analysis of the transmembrane topology of caleosins. Accordingly, the non-membrane class are the most abundant and diverse caleosins, especially in lower plants. Comparing the results with other reports suggests a stress response capacity for these caleosins. However, other classes play a more specific role in germination and pollination. A phylogenetic study also revealed two main clades that were significantly different in terms of caleosin type, expression profile, molecular weight, and isoelectric point (P < 0.01). In addition to the biochemical significance of the findings, predicting the structure of caleosins is necessary for constructing oil bodies used in the food and pharmaceutical industries.

Rice OsClo5, a caleosin protein, negatively regulates cold tolerance through the jasmonate signalling pathway

Caleosin is a lipid droplet-binding protein involved in maintenance of the lipid droplet structure and in signal transduction. However, the role of caleosin proteins in stress resistance is limited. Here, we report data for a rice caleosin protein gene, OsClo5, involved in cold stress tolerance via influence and regulation of the JA signalling pathway. Overexpression lines and RNAi lines of OsClo5 were subjected to cold stress and recovery to measure electrolyte leakage and survival rate. Changes were also detected in the genome-wide transcriptome of OsClo5 overexpressed plants. OsClo5 is located mainly in lipid droplets and expressed in all tissues tested. Its expression was upregulated by various stress conditions when subjected to cold treatment. Overexpression of OsClo5 decreased cold tolerance, and RNAi lines of OsClo5 had higher survival than WT seedlings. OsClo5 inhibited one jasmonate biosynthetic gene and several jasmonate ZIM domain (JAZ) genes, which were upregulated in response to cold stress. OsClo5 is a constitutively expressed caleosin protein that regulates plant cold resistance through inhibition of jasmonate signalling and JA synthesis.

Characterization and Expression Analyses of Callose Synthase Enzyme (Cals) Family Genes in Maize (Zea mays L.)

The callose synthase enzyme genes (Cals) generally plays an important role in resisting to environmental stresses as well as in regulating the microspore development of higher plant. However till now, few researches about ZmCals genes have been reported in maize. In this study, ten ZmCals genes were identified, and they are distributed on four chromosomes in maize. All ZmCals proteins contain Glucan-synthase-domain and Fks1-domain. RNA-seq data from public databases were analyzed and the result suggested that ZmCals involved in the development of various tissues, and a strong expression presented especially in young tissue. qRT-PCR analysis shown that most of ZmCals are highly expressed in root, stem and leaf at jointing stage (V6 stage) with maize inbred line B73. Seven out of 10 ZmCals genes display higher expression during maize anther development especially from stage 6 to stage 8b, the dynamic accumulation process of callose is also observed during these period with aniline blue staining. Above results indicated multiple ZmCals may participate in the deposition of callose in maize anther. Therefore, ZmCals are necessary not only for reproductive organ but also for nutritive organ during maize growth and development. This study lays certain foundation for further investigating the roles of the callose synthase enzymes genes in maize.

Gene atlas of iron-containing proteins in Arabidopsis thaliana

Iron (Fe) is an essential element for the development and physiology of plants, owing to its presence in numerous proteins involved in central biological processes. Here, we established an exhaustive, manually curated inventory of genes encoding Fe-containing proteins in Arabidopsis thaliana, and summarized their subcellular localization, spatiotemporal expression and evolutionary age. We have currently identified 1068 genes encoding potential Fe-containing proteins, including 204 iron-sulfur (Fe-S) proteins, 446 haem proteins and 330 non-Fe-S/non-haem Fe proteins (updates of this atlas are available at https://conf.arabidopsis.org/display/COM/Atlas+of+Fe+containing+proteins). A fourth class, containing 88 genes for which iron binding is uncertain, is indexed as 'unclear'. The proteins are distributed in diverse subcellular compartments with strong differences per category. Interestingly, analysis of the gene age index showed that most genes were acquired early in plant evolutionary history and have progressively gained regulatory elements, to support the complex organ-specific and development-specific functions necessitated by the emergence of terrestrial plants. With this gene atlas, we provide a valuable and updateable tool for the research community that supports the characterization of the molecular actors and mechanisms important for Fe metabolism in plants. This will also help in selecting relevant targets for breeding or biotechnological approaches aiming at Fe biofortification in crops.

Selection and Validation of Reference Genes for qRT-PCR Analysis in the Oil-Rich Tuber Crop Tiger Nut (Cyperus esculentus) Based on Transcriptome Data

Tiger nut (Cyperus esculentus), a perennial C₄ plant of the Cyperaceae family, is an unconventional crop that is distinguished by its oil-rich tubers, which also possesses the advantages of strong resistance, wide adaptability, short life periods, and large biomass. To facilitate studies on gene expression in this species, we identified and validated a series of reference genes (RGs) based on transcriptome data, which can be employed as internal controls for qRT-PCR analysis in tiger nut. Fourteen putative candidate RGs were identified and evaluated across nine different tissues of two cultivars, and the RGs were analyzed using three different algorithms (geNorm, NormFinder, and BestKeeper). The stability rankings of the candidate RGs were merged into consensus lists with RankAggreg. For the below-ground storage organ of tiger nut, the optimal RGs were TUB4 and UCE2 in different developmental stages of tubers. UCE2 and UBL5 were the most stably expressed RGs among all tissues, while Rubisco and PGK exhibited the lowest expression stability. UCE2, UBL5 and Rubisco were compared to normalize the expression levels of the caleosin (CLO) and diacylglycerol acyltransferase 2-2 (DGAT2-2) genes across the same tissues. Our results showed that the RGs identified in this study, which exhibit more uniform expression patterns, may be utilized for the normalization of qRT-PCR results, promoting further research on gene expression in various tissues of tiger nut.

OsClo5 functions as a transcriptional co-repressor by interacting with OsDi19-5 to negatively affect salt stress tolerance in rice seedlings

Caleosins constitute a small protein family with one calcium-binding EF-hand motif. They are involved in the regulation of development and response to abiotic stress in plants. Nevertheless, how they impact salt stress tolerance in rice is largely unknown. Thereby, biochemical and molecular genetic experiments were carried out, and the results revealed that OsClo5 was able to bind calcium and phospholipids in vitro and localized in the nucleus and endoplasmic reticulum in rice protoplasts. At the germination and early seedlings stages, overexpression transgenic lines and T-DNA mutant lines exhibited reduced and increased tolerance to salt stress, respectively, compared with the wild-type. Yeast two-hybrid, bimolecular fluorescence complementation and in vitro pull-down assays demonstrated that the EF-hand motif of OsClo5 was essential for the interactions with itself and OsDi19-5. Yeast one-hybrid, electrophoretic migration shift and dual-luciferase reporter assays identified OsDi19-5 as a transcriptional repressor via the TACART cis-element in the promoters of two salt stress-related target genes, OsUSP and OsMST. In addition, OsClo5 enhanced the inhibitory effect of OsDi19-5 in the tobacco transient system, which was confirmed by qRT-PCR analysis in rice seedlings under salt stress. The collective results deepen the understanding of the molecular mechanism underlying the roles of caleosin in the salt stress response. These findings will also inform efforts to improve salt tolerance of rice.

Evolution and Stress Responses of CLO Genes and Potential Function of the GhCLO06 Gene in Salt Resistance of Cotton

The caleosin (CLO) protein family displays calcium-binding properties and plays an important role in the abiotic stress response. Here, a total of 107 CLO genes were identified in 15 plant species, while no CLO genes were detected in two green algal species. Evolutionary analysis revealed that the CLO gene family may have evolved mainly in terrestrial plants and that biological functional differentiation between species and functional expansion within species have occurred. Of these, 56 CLO genes were identified in four cotton species. Collinearity analysis showed that CLO gene family expansion mainly occurred through segmental duplication and whole-genome duplication in cotton. Sequence alignment and phylogenetic analysis showed that the CLO proteins of the four cotton species were mainly divided into two types: H-caleosins (class I) and L-caleosins (class II). Cis-acting element analysis and quantitative RT-PCR (qRT-PCR) suggested that GhCLOs might be regulated by abscisic acid (ABA) and methyl jasmonate (MeJA). Moreover, transcriptome data and qRT-PCR results revealed that GhCLO genes responded to salt and drought stresses. Under salt stress, gene-silenced plants (TRV: GhCLO06) showed obvious yellowing and wilting, higher malondialdehyde (MDA) content accumulation, and significantly lower activities of superoxide dismutase (SOD) and peroxidase (POD), indicating that GhCLO06 plays a positive regulatory role in cotton salt tolerance. In gene-silenced plants (TRV: GhCLO06), ABA-related genes (GhABF2, GhABI5, and GhNAC4) were significantly upregulated after salt stress, suggesting that the regulation of salt tolerance may be related to the ABA signaling pathway. This research provides an important reference for further understanding and analyzing the molecular regulatory mechanism of CLOs for salt tolerance.

Label-Free Quantitative Phosphoproteomics Reveals Signaling Dynamics Involved in Embryogenic Competence Acquisition in Sugarcane

In this study, a label-free quantitative phosphoproteomic analysis was performed to identify and quantify signaling events related to the acquisition of embryogenic competence in sugarcane. Embryogenic and nonembryogenic calli were compared at the multiplication phase, resulting in the identification of 163 phosphoproteins unique to embryogenic calli, 9 unique to nonembryogenic calli, and 51 upregulated and 40 downregulated in embryogenic calli compared to nonembryogenic calli. Data are available via ProteomeXchange with identifier PXD018054. Motif-x analysis revealed the enrichment of [xxxpSPxxx], [RxxpSxxx], and [xxxpSDxxx] motifs, which are predicted phosphorylation sites for several kinases related to stress responses. The embryogenic-related phosphoproteins (those unique and upregulated in embryogenic calli) identified in the present study are related to abscisic acid-induced signaling and abiotic stress response; they include OSK3, ABF1, LEAs, and RD29Bs. On the other hand, the nonembryogenic-related phosphoproteins EDR1 and PP2Ac-2 are negative regulators of abscisic acid signaling, suggesting a relationship between phosphoproteins involved in the abscisic acid and stress responses in the acquisition of embryogenic competence. Moreover, embryogenic-related phosphoproteins associated with epigenetic modifications, such as HDA6, HDA19, and TOPLESS, and with RNA metabolism, including AGO1, DEAH5, SCL30, UB2C, and SR45, were identified to play potential roles in embryogenic competence. These results reveal novel phosphorylation sites for several proteins and identify potential candidate biomarkers for the acquisition of embryogenic competence in sugarcane.

Genome-wide analysis of the callose enzyme families of fertile and sterile flower buds of the Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Callose is a β‐1,3‐glucan commonly found in higher plants that plays an important role in regulating plant pollen development. It is synthesized by glucan synthase‐like (GSL) and is degraded by the enzyme endo‐1,3‐β‐glucosidase. However, genome‐wide analyses of callose GSL and endo‐1,3‐β‐glucosidase enzymes in fertile and sterile flower buds of Chinese cabbage have not yet been reported. Here, we show that delayed callose degradation at the tetrad stage may be the main cause of microspore abortion in Chinese cabbage with nuclear sterility near‐isogenic line ‘10L03’. Fifteen callose GSLs and 77 endo‐1,3‐β‐glucosidase enzymes were identified in Chinese cabbage. Phylogenetic, gene structural and chromosomal analyses revealed that the expansion occurred due to three polyploidization events of these two gene families. Expression pattern analysis showed that the GSL and endo‐1,3‐β‐glucosidase enzymes are involved in the development of various tissues and that the genes functionally diverged during long‐term evolution. Relative gene expression analysis of Chinese cabbage flowers at different developmental stages showed that high expression of the synthetic enzyme BraA01g041620 and low expression of AtA6‐homologous genes (BraA04g008040, BraA07g009320, BraA01g030220 and BraA03g040850) and two other genes (BraA10g020080 and BraA05g038340) for degrading enzymes in the meiosis and tetrad stages may cause nuclear sterility in the near‐isogenic line ‘10L03’. Overall, our data provide an important foundation for comprehending the potential roles of the callose GSL and endo‐1,3‐β‐glucosidase enzymes in regulating pollen development in Chinese cabbage.

Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae

Bioinformatics analyses of caleosin/peroxygenases (CLO/PXG) demonstrated that these genes are present in the vast majority of Viridiplantae taxa for which sequence data are available. Functionally active CLO/PXG proteins with roles in abiotic stress tolerance and lipid droplet storage are present in some Trebouxiophycean and Chlorophycean green algae but are absent from the small number of sequenced Prasinophyceaen genomes. CLO/PXG-like genes are expressed during dehydration stress in Charophyte algae, a sister clade of the land plants (Embryophyta). CLO/PXG-like sequences are also present in all of the >300 sequenced Embryophyte genomes, where some species contain as many as 10–12 genes that have arisen via selective gene duplication. Angiosperm genomes harbour at least one copy each of two distinct CLO/PX isoforms, termed H (high) and L (low), where H-forms contain an additional C-terminal motif of about 30–50 residues that is absent from L-forms. In contrast, species in other Viridiplantae taxa, including green algae, non-vascular plants, ferns and gymnosperms, contain only one (or occasionally both) of these isoforms per genome. Transcriptome and biochemical data show that CLO/PXG-like genes have complex patterns of developmental and tissue-specific expression. CLO/PXG proteins can associate with cytosolic lipid droplets and/or bilayer membranes. Many of the analysed isoforms also have peroxygenase activity and are involved in oxylipin metabolism. The distribution of CLO/PXG-like genes is consistent with an origin >1 billion years ago in at least two of the earliest diverging groups of the Viridiplantae, namely the Chlorophyta and the Streptophyta, after the Viridiplantae had already diverged from other Archaeplastidal groups such as the Rhodophyta and Glaucophyta. While algal CLO/PXGs have roles in lipid packaging and stress responses, the Embryophyte proteins have a much wider spectrum of roles and may have been instrumental in the colonisation of terrestrial habitats and the subsequent diversification as the major land flora.

Genome-wide analysis indicates diverse physiological roles of the turnip (Brassica rapa var. rapa) oligopeptide transporters gene family

Oligopeptide transporters (OPTs) encode integral membrane-localized proteins and have a broad range of substrate transport capabilities. Here, 28 BrrOPT genes were identified in the turnip. Phylogenetic analyses revealed two well-supported clades in the OPT family, containing 15 BrrOPTs and 13 BrrYSLs. The exon/intron structure of OPT clade are conserved but the yellow stripe-like (YSL) clade was different. The exon/intron of the YSL clade possesses structural differences, whereas the YSL class motifs structure are conserved. The OPT genes are distributed unevenly among the chromosomes of the turnip genome. Phylogenetic and chromosomal distribution analyses revealed that the expansion of the OPT gene family is mainly attributable to segmental duplication. For the expression profiles at different developmental stages, a comprehensive analysis provided insights into the possible functional divergence among members of the paralog OPT gene family. Different expression levels under a variety of ion deficiencies also indicated that the OPT family underwent functional divergence during long-term evolution. Furthermore, BrrOPT8.1, BrrYSL1.2, BrrYSL1.3, BrrYSL6 and BrrYSL9 responded to Fe(II) treatments and BrrYSL7 responded to calcium treatments, BrrYSL6 responded to multiple treatments in root, suggesting that turnip OPTs may be involved in mediating cross-talk among different ion deficiencies. Our data provide important information for further functional dissection of BrrOPTs, especially in transporting metal ions and nutrient deficiency stress adaptation.

Specific Caleosin/Peroxygenase and Lipoxygenase Activities Are Tissue-Differentially Expressed in Date Palm (Phoenix dactylifera L.) Seedlings and Are Further Induced Following Exposure to the Toxin 2,3,7,8-tetrachlorodibenzo-p-dioxin

Two caleosin/peroxygenase isoforms from date palm, Phoenix dactylifera L., PdCLO2 and PdCLO4, were characterized with respect to their tissue expression, subcellular localization, and oxylipin pathway substrate specificities in developing seedlings. Both PdCLO2 and PdCLO4 had peroxygenase activities that peaked at the mid-stage (radicle length of 2.5 cm) of seedling growth and were associated with the lipid droplet (LD) and microsomal fractions. Recombinant PdCLO2 and PdCLO4 proteins heterologously expressed in yeast cells were localized in both LD and microsomal fractions. Each of the purified recombinant proteins exhibited peroxygenase activity but they were catalytically distinct with respect to their specificity and product formation from fatty acid epoxide and hydroxide substrates. We recently showed that date palm CLO genes were upregulated following exposure to the potent toxin, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) (Hanano et al., 2016), and we show here that transcripts of 9- and 13-lipoxygenase (LOX) genes were also induced by TCDD exposure. At the enzyme level, 9-LOX and 13-LOX activities were present in a range of seedling tissues and responded differently to TCDD exposure, as did the 9- and 13-fatty acid hydroperoxide reductase activities. This demonstrates that at least two branches of the oxylipin pathway are involved in responses to the environmental organic toxin, TCDD in date palm.