Genome-wide identification,systematic analysis and characterization of <Emphasis Type="Italic">SRO</Emphasis> family genes in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

SIMILAR TO RCD ONE (SRO) is a small plant-specific gene family, which play essential roles in plant growth and development as well as in abiotic stresses. However, the function of SROs in maize is still unknown. In our study, six putative SRO genes were isolated from the maize genome. A systematic analysis was performed to characterize the ZmSRO gene family. The ZmSRO gene family was divided into two groups according to the motif and intron/exon analysis. Phylogenetic analysis of them with other plants showed that the clades of SROs along with the divergence of monocot and dicot and ZmSROs were more closely with OsSROs. Many abiotic stress response and hormone-induced cis-regulatory elements were identified from the promoter region of ZmSROs. Furthermore, RNA-seq analysis indicated that SRO genes were widely expressed in different tissues and development stages in maize, and the expression divergence was also obviously observed. Analyses of expression in response to PEG6000 and NaCl treatment, in addition to exogenous application of ABA and GA hormones showed that the majority of the members display stress-induced expression patterns. Taken together, our results provide valuable reference for further functional analysis of the SRO gene family in maize, especially in abiotic stress responses.     

Late Embryogenesis Abundant (<Emphasis Type="Italic">LEA</Emphasis>) Gene Family in Maize: Identification,Evolution, and Expression Profiles

Late embryogenesis abundant (LEA) proteins are identified as a large and highly diverse group of polypeptides accumulating in response to cellular dehydration in many organisms. However, there are only very limited reports of this protein family in maize until this study. In the present paper, we identified 32 LEA genes in maize. A total of 83 LEA proteins including 51 members in Arabidopsis and 32 putative members in maize were classified into nine groups. Gene organization and motif compositions of the LEA members are highly conserved in each of the groups, indicative of their functional conservation. The predicted ZmLEA genes were non-random distributed across chromosomes, and transposition event and segmental duplication contributed to the expansion of the LEA gene family in maize. Some abiotic stress-responsive cis-elements were also found in the promoters of ZmLEA genes. Microarray expression analyses revealed different accumulation patterns of ZmLEA family members. Moreover, some members of ZmLEAs were regulated under IAA and some abiotic stresses. This study will provide comprehensive information for maize LEA gene family and may pave the way for deciphering their functions in further studies.     

Genome-wide identification and characterization of the RIO atypical kinase family in plants

Members of the right open reading frame (RIO) atypical kinase family are present in all three domains of life. In eukaryotes, three subfamilies have been identified: RIO1, RIO2, and RIO3. Studies have shown that the yeast and human RIO1 and RIO2 kinases are essential for the biogenesis of small ribosomal subunits. Thus far, RIO3 has been found only in multicellular eukaryotes. In this study, we systematically identified members of the RIO gene family in 37 species representing the major evolutionary lineages in Viridiplantae. A total of 84 RIO genes were identified; among them, 41 were classified as RIO1 and 43 as RIO2. However, no RIO3 gene was found in any of the species examined. Phylogenetic trees constructed for plant RIO1 and RIO2 proteins were generally congruent with the species phylogeny. Subcellular localization analyses showed that the plant RIO proteins were localized mainly in the nucleus and/or cytoplasm. Expression profile analysis of rice, maize, and Arabidopsis RIO genes in different tissues revealed similar expression patterns between RIO1 and RIO2 genes, and their expression levels were high in certain tissues. In addition, the expressions of plant RIO genes were regulated by two drugs: mycophenolic acid and actinomycin D. Function prediction using genome-wide coexpression analysis revealed that most plant RIO genes may be involved in ribosome biogenesis. Our results will be useful for the evolutionary analysis of the ancient RIO kinase family and provide a basis for further functional characterization of RIO genes in plants.     

Genomewide analysis of <Emphasis Type="Italic">MATE</Emphasis>-type gene family in maize reveals microsynteny and their expression patterns under aluminum treatment

Multidrug and toxic compound extrusion (MATE) proteins are a group of secondary active transporters, which widely exist in all living organisms and play important role in the detoxication of endogenous secondary metabolites and exogenous agents. However, to date, no systematic and comprehensive study of this family is reported in maize. Here, a total of 49 MATE genes (ZmMATE) were identified and divided into seven groups by phylogenetic analysis. Conserved intro–exon structures and motif compositions were investigated in these genes. Results by gene locations indicated that these genes were unevenly distributed among all 10 chromosomes. Tandem and segmental duplications appeared to contribute to the expansion and evolution of this gene family. The K_a/ K_s ratios suggested that the ZmMATE has undergone large-scale purifying selection on the maize genome. Interspecies microsynteny analysis revealed that there were independent gene duplication events of 10 ZmMATE. In addition, most maize MATE genes exhibited different expression profiles in diverse tissues and developmental stages. Sixteen MATE genes were chosen for further quantitative real-time polymerase chain reaction analysis showed differential expression patterns in response to aluminum treatment. These results provide a useful clue for future studies on the identification of MATE genes and functional analysis of MATE proteins in maize.     

LcMKK,a MAPK kinase from <Emphasis Type="Italic">Lycium chinense</Emphasis>, confers cadmium tolerance in transgenic tobacco by transcriptional upregulation of ethylene responsive transcription factor gene

Cadmium (Cd) is a highly toxic element to plants. Ethylene is an important phytohormone in the regulation of plant growth, development and stress response. Mitogen-activated protein kinase (MAPK) activation has been observed in plants exposed to Cd stress and was suggested to be involved in ethylene biosynthesis. We hypothesized that there may be a link between MAPK cascades and ethylene signalling in Cd-stressed plants. To test this hypothesis, the expression of LcMKK, LchERF and LcGSH1 genes, endogenous ethylene accumulation, GSH content and Cd concentration in Lycium chinense with or without Cd stress treatment were studied. Our results showed that LcMKK gene expression can be induced by the treatment of Cd in L. chinense. The transgenic tobacco expressing 35S::LcMKK showed greater tolerance to Cd stress and enhanced expression of NtERF and NtGSH1 genes, indicating that LcMKK is associated with the enhanced expression level of ERF and GSH synthesis-related genes in tobacco. We also found that endogenous ethylene and GSH content can be induced by Cd stress in L. chinense, and inhibited by cotreatment with PD98059, an inhibitor of MAPK kinase. Evidences presented here suggest that under Cd stress, GSH accumulation occurred at least partially by enhanced LcMKK gene expression and the ethylene signal transduction pathways might be involved in this accumulation.     

Vernalization and Photoperiods Mediated IAA and ABA Synthesis Genes Expression in <Emphasis Type="Italic">Beta vulgaris</Emphasis>

Biennial plants perceived seasonal stimuli through the photoperiods and vernalization pathways respectively to optimize developmental time. Photoperiods combining with vernalization modulate hormone homeostasis to promote plant normally growth. IAA and ABA play important roles in plant development. Although a series of IAA and ABA genes and their regulation mechanisms have been investigated and characterized extensively in model plants, these underlined mechanisms in Beta vulgaris L. especially under abiotic stress were not entirely clear. This study aimed at exploring IAA and ABA biosynthetic pathway genes and investigating their expression patterns and quantitating analysis hormone by UPLC-MS/MS (ultra performance liquid chromatography-tandem mass spectrometry) in order to demonstrate the molecular mechanism of phytohormone in B. vulgaris. As the results showed BvNIT4 and BvIAA8 contributed to IAA accumulation under nonvernalization condition. Endogenous ABA accumulation in leaves was contributed coordinately by the expression of BvABA2 and BvNCED1 genes both in the vernalized and nonvernalized samples under long day conditions. Vernalization and photoperiods indeed disturb phytohormone genes expression patterns, which data were consistent with the previous studies. New insight was provided to further clarify the molecular mechanism of endogenous hormone in B. vulgaris.     

Genome-wide identification and abiotic stress responses of <Emphasis Type="Italic">DGK</Emphasis> gene family in maize

Diacylglycerol kinase (DGK) is a kind of phosphokinase that catalyzes the formation of signaling molecule phosphatidic acid. In this study, seven maize (Zea mays) DGK gene family members were identified by an exploration of maize genome via multiple online databases, and designated as ZmDGK1-7, respectively. The proteins encoded by ZmDGKs ranged from 487 to 716 amino acids, and had a molecular weight (MWs) between 54.6 and 80.2 kDa. Phylogenetic analysis revealed that ZmDGKs grouped into three clusters as described for known plant DGK families: Cluster I was composed of three maize DGKs, ZmDGK1, ZmDGK4 and ZmDGK5, cluster II contained ZmDGK6, and the isoforms ZmDGK2, ZmDGK3 and ZmDGK7 fell into cluster III. ZmDGK proteins featured the typical functional domains, while all seven ZmDGKs have a conserved catalytic domain DGKc, only the cluster I ZmDGKs have the DAG/PE binding domain. Most ZmDGK genes showed ubiquitous expression profiles at various developmental stages, while a high relative expression was observed at the tasseling stage. ZmDGK genes exhibited differential expression patterns in response to abiotic stresses including cold, salinity and drought, and all ZmDGK genes were found obviously up-regulated by cold. The distinct roles of ZmDGKs in cold response was also supported by the finding that an accumulation of DGK products–PA under low temperature. This study will help to better understand the roles of DGKs in the development and abiotic stress responses in major crops.     

Expression Profiling of the <Emphasis Type="Italic">CSDP</Emphasis> Transcription Factor Gene Family Points to Roles in Organ Development and Abiotic Stress Response in Tomato (<Emphasis Type="Italic">Solanum lycopersicum</Emphasis> L.)

The cold shock domain proteins (CSDPs) are small group of nucleic acid-binding proteins that act as RNA chaperones in growth regulation, development, and stress adaptation in plants. The functions of CSDPs have been studied in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), wheat (Triticum aestivum), and Chinese cabbage (Brassica rapa). To gain insight into the function of CSDPs in tomato (Solanum lycopersicum), we performed a genome-wide analysis of CSDPs through in silico characterization and expression profiling in different organs and in response to different abiotic stress and phytohormone treatments. We identified five non-redundant SlCSDP genes. The evolutionary analysis and phylogenetic classification indicated that tomato CSDPs are more closely related to potato than those of others. The five SlCSDP genes are distributed on four of the 12 tomato chromosomes and no segmental or tandem duplication events are detected among them. Expression analysis showed broad expression patterns with strong expression in fruit development and ripening. Expression of individual SlCSDP genes was significantly altered by stress and phytohormone treatments. SlCSDP2, SlCSDP3, and SlCSDP4 were highly induced by all four abiotic stresses and by phytohormone treatment in tomato. These findings provide a foundation for future research towards functional biological roles of CSDP gene in particular to develop tomato cultivars with large size, early ripening, and abiotic stress tolerance.     

Genome-wide analysis and expression profiling of the phospholipase D gene family in Gossypium arboreum

The plant phospholipase D(PLD)plays versatile functions in multiple aspects of plant growth,development,and stress responses.However,until now,our knowledge concerning the PLD gene family members and their expression patterns in cotton has been limited.In this study,we performed for the first time the genome-wide analysis and expression profiling of PLD gene family in Gossypium arboretum,and finally,a total of 19 non-redundant PLD genes(GaPLDs)were identified.Based on the phylogenetic analysis,they were divided into six well-supported clades(α,β/γ,δ,ε,ζ and φ).Most of the GaPLD genes within the same clade showed the similar exon-intron organization and highly conserved motif structures.Additionally,the chromosomal distribution pattern revealed that GaPLD genes were unevenly distributed across 10 of the 13 cotton chromosomes.Segmental duplication is the major contributor to the expansion of Ga PLD gene family and estimated to have occurred from19.61 to 20.44 million years ago when a recent large-scale genome duplication occurred in cotton.Moreover,the expression profiling provides the functional divergence of GaPLD genes in cotton and provides some new light on the molecular mechanisms of GaPLDα1 and GaPLDδ2 in fiber development.