Hongyan Su

Genome-wide analysis of NAM-ATAF1,2-CUC2 transcription factor family in Solanum lycopersicum

NAM, ATAF1,2, and CUC2 (NAC) proteins constitute one of the largest families of plant-specific transcription factors. These proteins have diverse functions in biological processes. Particularly, NAC transcription factors have received considerable attention as regulators in stress signaling pathways. However, little is known about the NAC genes in tomato (Solanum lycopersicum). In this study, 104 NAC genes were identified in the tomato genome. The predicted NAC genes were distributed across all of 12 chromosomes at various densities and were phylogenetically clustered into six groups (I–VI), together with NAC genes from Arabidopsis and rice.The structure and motif compositions of the NAC genes in tomato were also analyzed. Analysis of available microarray data showed that most of the NAC genes in tomato had specific temporal and spatial expression patterns. Moreover, the expression profiles of eight selected NAC genes in tomato were analyzed in different tissues under different abiotic conditions by quantitative real-time RT-PCR. Except for one, all eight selected genes responded to one or more of the abiotic stress treatments. The results of this study provided insights into the classification and putative functions of this family.

Differential expression profiles of poplar MAP kinase kinases in response to abiotic stresses and plant hormones, and overexpression of PtMKK4 improves the drought tolerance of poplar.

Mitogen-activated protein kinase (MAPK) cascades are universal signal transduction modules that play essential roles in plant growth, development and stress response. MAPK kinases (MAPKKs), which link MAPKs and MAPKK kinases (MAPKKKs), are integral in mediating various stress responses in plants. However, to date few data about the roles of poplar MAPKKs in stress signal transduction are available. In this study, we performed a systemic analysis of poplar MAPKK gene family expression profiles in response to several abiotic stresses and stress-associated hormones. Furthermore, Populus trichocarpa MAPKK4 (PtMKK4) was chosen for functional characterization. Transgenic analysis showed that overexpression of the PtMKK4 gene remarkably enhanced drought stress tolerance in the transgenic poplar plants. The PtMKK4-overexpressing plants also exhibited much lower levels of H2O2 and higher antioxidant enzyme activity after exposure to drought stress compared to the wide type lines. Besides, some drought marker genes including PtP5CS, PtSUS3, PtLTP3 and PtDREB8 exhibited higher expression levels in the transgenic lines than in the wide type under drought conditions. This study provided valuable information for understanding the putative functions of poplar MAPKKs involved in important signaling pathways under different stress conditions.

Global analysis of ankyrin repeat domain C3HC4-type RING finger gene family in plants.

Ankyrin repeat (ANK) C3HC4-type RING finger (RF) genes comprise a large family in plants and play important roles in various physiological processes of plant life. In this study, we identified 187 ANK C3HC4-type RF proteins from 29 species with complete genomes and named the ANK C3HC4-type RF proteins the XB3-like proteins because they are structurally related to the rice (Oryza sativa) XB3. A phylogenetic relationship analysis suggested that the XB3-like genes originated from ferns, and the encoded proteins fell into 3 major groups. Among these groups, we found that the spacing between the metal ligand position 6 and 7, and the conserved residues, which was in addition to the metal ligand amino acids, in the C3HC4-type RF were different. Using a wide range of protein structural analyses, protein models were established, and all XB3-like proteins were found to contain two to seven ANKs and a C3HC4-type RF. The microarray data for the XB3-like genes of Arabidopsis, Oryza sative, Zea mays and Glycine max revealed that the expression of XB3-like genes was in different tissues and during different life stages. The preferential expression of XB3-like genes in specified tissues and the response to phytohormone and abiotic stress treatments of Arabidopsis and Zea mays not only confirmed the microarray analysis data but also demonstrated that the XB3-like proteins play roles in plant growth and development as well as in stress responses. Our data provide a very useful reference for the identification and functional analysis of members of this gene family and also provide a new method for the genome-wide analysis of gene families.

Superfamily of ankyrin repeat proteins in tomato.

The ankyrin repeat (ANK) protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, no detailed information concerning this family is available for tomato (Solanum lycopersicum) due to the limited information on whole genome sequences. In this study, we identified a total of 130 ANK genes in tomato genome (SlANK), and these genes were distributed across all 12 chromosomes at various densities. And chromosomal localizations of SlANK genes indicated 25 SlANK genes were involved in tandem duplications. Based on their domain composition, all of the SlANK proteins were grouped into 13 subgroups. A combined phylogenetic tree was constructed with the aligned SlANK protein sequences. This tree revealed that the SlANK proteins comprise five major groups. An analysis of the expression profiles of SlANK genes in tomato in different tissues and in response to stresses showed that the SlANK proteins play roles in plant growth, development and stress responses. To our knowledge, this is the first report of a genome-wide analysis of the tomato ANK gene family. This study provides valuable information regarding the classification and putative functions of SlANK genes in tomato.

Overexpression of a Populus trichocarpa H+-pyrophosphatase gene PtVP1.1 confers salt tolerance on transgenic poplar

The Arabidopsis vacuolar H(+)-pyrophosphatase (AVP1) has been well studied and subsequently employed to improve salt and/or drought resistance in herbaceous plants. However, the exact function of H(+)-pyrophosphatase in woody plants still remains unknown. In this work, we cloned a homolog of type I H(+)-pyrophosphatase gene, designated as PtVP1.1, from Populus trichocarpa, and investigated its function in both Arabidopsis and poplar. The deduced translation product PtVP1.1 shares 89.74% identity with AVP1. Semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) and quantitative real-time PCR analyses revealed a ubiquitous expression pattern of PtVP1.1 in various tissues, including roots, stems, leaves and shoot tips. Heterologous expression of PtVP1.1 rescued the retarded-root-growth phenotype of avp1, an Arabidopsis knock out mutant of AVP1, on low carbohydrate medium. Overexpression of PtVP1.1 in poplar (P. davidiana × P. bolleana) led to more vigorous growth of transgenic plants in the presence of 150 mM NaCl. Microsomal membrane vesicles derived from PtVP1.1 transgenic plants exhibited higher H(+)-pyrophosphatase hydrolytic activity than those from wild type (WT). Further studies indicated that the improved salt tolerance was associated with a decreased Na(+) and increased K(+) accumulation in the leaves of transgenic plants. Na(+) efflux and H(+) influx in the roots of transgenic plants were also significantly higher than those in the WT plants. All these results suggest that PtVP1.1 is a functional counterpart of AVP1 and can be genetically engineered for salt tolerance improvement in trees.

Overexpression of the NDR1/HIN1-Like Gene NHL6 Modifies Seed Germination in Response to Abscisic Acid and Abiotic Stresses in Arabidopsis

NHL (NDR1/HIN1-like) genes play crucial roles in pathogen induced plant responses to biotic stress. Here, we report the possible function of NHL6 in plant response to abscisic acid (ABA) and abiotic stress. NHL6 was highly expressed in non-germinated seeds, and its expression was strongly induced by ABA and multiple abiotic stress signals. Loss-of-function of NHL6 decreased sensitivity to ABA in the early developmental stages including seed germination and post-germination seedling growth of the nhl6 mutants. However, overexpression of NHL6 increased sensitivity to ABA, salt and osmotic stress of the transgenic plants. Further studies indicated that the increased sensitivity in the 35S::NHL6 overexpressing plants could be a result of both ABA hypersensitivity and increased endogenous ABA accumulation under the stress conditions. It was also seen that the ABA-responsive element binding factors AREB1, AREB2 and ABF3 could regulate NHL6 expression at transcriptional level. Our results indicate that NHL6 plays an important role in the abiotic stresses-induced ABA signaling and biosynthesis, particularly during seed germination and early seedling development in Arabidopsis.

Making good use of the byproducts of cultivation: green synthesis and antibacterial effects of silver nanoparticles using the leaf extract of blueberry

In this study, we made an effort to use blueberry leaves extract as a reducing and a capping agent to biosynthesize silver nanoparticles (AgNPs). The successful formation of AgNPs was confirmed with UV–visible spectroscopy, transmission electron microscopy, Fourier transform infrared spectroscopy and X-ray diffraction. Furthermore, their antimicrobial activities against four kinds of multi drug resistant clinical pathogens and aquatic pathogens were investigated. The results showed that as-prepared AgNPs exhibited broad-spectrum antibacterial activities. The antibacterial effects of the AgNPs based on the structural damage and DNA degradation of the tested bacteria were also studied. The green synthesis of AgNPs using blueberry leaf extract, which provided a new idea on the use of the byproducts of blueberry harvesting.

Overexpression of PeMIPS1 confers tolerance to salt and copper stresses by scavenging reactive oxygen species in transgenic poplar

Myo-inositol is a vital compound in plants. As the key rate-limiting enzyme in myo-inositol biosynthesis, l-myo-inositol-1-phosphate synthase (MIPS) is regarded as a determinant of the myo-inositol content in plants. The up-regulation of MIPS genes can increase the myo-inositol content, thereby enhancing the plants resistance to a variety of stresses. However, there are few reports on the roles of myo-inositol and the identification of MIPS in woody trees. In this study, a MIPS gene, named as PeMIPS1, was characterized from Populus euphratica Oliv. The heterologous expression of PeMIPS1 compensated for inositol production in the yeast inositol auxotrophic mutant ino1 and the phenotypic lesions of the atmips1-2 mutant, an Arabidopsis MIPS1 knock-out mutant. A subcellular location analysis showed that the PeMIPS1-GFP fusion was localized in the nucleus and cytoplasm, but not in the chloroplasts, indicating that PeMIPS1 represented the cytosolic form of MIPS in P. euphratica. Interestingly, PeMIPS1 was not only inducible by drought and high salinity, but also by CuSO4 treatment. The transgenic poplar lines overexpressing PeMIPS1 had greater plant heights, shoot biomasses and survival rates than the wild type during the salt- or copper-stress treatment, and this was accompanied by an increase in the myo-inositol content. The overexpression of PeMIPS1 resulted in the increased activities of antioxidant enzymes and the accumulation of ascorbate, a key nonenzymatic antioxidant in plant, which partly accounted for the enhanced reactive oxygen species-scavenging capacity and the lowered hydrogen peroxide and malondialdehyde levels in the transgenic poplar. To the best of our knowledge, this study is the first to report the roles of MIPS genes in the tolerance to copper stress.