Molecular mechanism of leaf adaxial upward curling caused by BpPIN3 suppression in Betula pendula.

Leaves are one of the vegetative organs of plants that are essential for plant growth and development. PIN-FORMED (PINs) gene is an indoleacetic acid (IAA) transporter that plays a critical role in leaf development. To determine the function of BpPIN3 in leaf polarity formation in Betula pendula, the transgenic lines with BpPIN3 overexpression (OE) and BpPIN3-reduced expression (RE) were analyzed using the Agrobacterium-mediated method. The RE lines displayed the characteristics of leaf margin adaxial upward curling, with lower expression of BpPIN3 resulting in greater rolling. Tissue localization of IAA in the auxin GUS reporter system proved that auxin in the RE was mainly distributed in the secondary veins, palisade tissues, and epidermal cells in the leaf margin area. The auxin content in the leaf margin area was significantly greater than that in the main vein tissue. The cell density of the palisade tissue and the ratio of palisade tissue to spongy tissue in the curled leaf margin of the RE lines were found to be significantly decreased. RNA-seq analysis revealed that the RE hormone-signaling pathway genes were significantly enriched compared with those of the OE and WT lines; in particular, the auxin response-related genes SAURs (i.e., SAUR23, SAUR24, SAUR28, and SAUR50) and GH3.10 were found to be significantly upregulated. qRT-PCR analysis indicated that BpPIN3 expression at the leaf margin was significantly lower than that near the main vein in the RE lines. In contrast, the expression levels of SAURs and GH3.10 were significantly higher than those near the midrib. In conclusion, BpPIN3 regulates the expression of auxin response-related genes and the polar transport of auxin to change the polar form of the proximal and distal axes of birch leaves.

PsnWRKY70 Negatively Regulates NaHCO3 Tolerance in Populus.

Poplar is an important afforestation and ornamental tree species in Northeast China. The distribution area of saline-alkali land is approximately 765 hm2 in Northeast China. The breeding of saline-alkali-resistant transgenic trees could be an effective method of afforestation in saline-alkali land. WRKY transcription factors play a crucial role in abiotic stress. In this study, we analyzed the genetic stability of the two-year-old PsnWRKY70 transgenic poplars. The results showed that PsnWRKY70 of transgenic poplars had been expressed stably and normally at the mRNA level. The gene interference expression (RE) lines had no significant effect on the growth of PsnWRKY70 under NaHCO3 stress, and the alkali damage index of RE lines was significantly lower than that of WT and overexpression (OE) lines at day 15 under NaHCO3 stress. POD activity was significantly higher in RE lines than in WT. The MDA content of the RE line was lower than that of the WT line. Transcriptome analysis showed that RE lines up-regulated genes enriched in cell wall organization or biogenesis pathway-related genes such as EXPA8, EXPA4, EXPA3, EXPA1, EXPB3, EXP10, PME53, PME34, PME36, XTH9, XTH6, XTH23, CESA1, CESA3, CES9; FLA11, FLA16 and FLA7 genes. These genes play an important role in NaHCO3 stress. Our study showed that the interference expression of the PsnWRKY70 gene can enhance the tolerance of NaHCO3 in poplar.

Corrigendum: Digital Gene Expression Analysis of Populus simonii × P. nigra Pollen Germination and Tube Growth.

[This corrects the article on p. 825 in vol. 7, PMID: 27379121.].

Digital Gene Expression Analysis of Populus simonii × P. nigra Pollen Germination and Tube Growth.

Pollen tubes are an ideal model for the study of cell growth and morphogenesis because of their extreme elongation without cell division; however, the genetic basis of pollen germination and tube growth remains largely unknown. Using the Illumina/Solexa digital gene expression system, we identified 13,017 genes (representing 28.3% of the unigenes on the reference genes) at three stages, including mature pollen, hydrated pollen, and pollen tubes of Populus simonii × P. nigra. Comprehensive analysis of P. simonii × P. nigra pollen revealed dynamic changes in the transcriptome during pollen germination and pollen tube growth (PTG). Gene ontology analysis of differentially expressed genes showed that genes involved in functional categories such as catalytic activity, binding, transporter activity, and enzyme regulator activity were overrepresented during pollen germination and PTG. Some highly dynamic genes involved in pollen germination and PTG were detected by clustering analysis. Genes related to some key pathways such as the mitogen-activated protein kinase signaling pathway, regulation of the actin cytoskeleton, calcium signaling, and ubiquitin-mediated proteolysis were significantly changed during pollen germination and PTG. These data provide comprehensive molecular information toward further understanding molecular mechanisms underlying pollen germination and PTG.

[Macrobenthic community structure of intertidal zone of Rushan Bay in spring].

Quantitative study on macrobenthos was carried out in 8 transects along intertidal zone of Rushan Bay in May, 2011. In total, 116 macrobenthic species were identified, among which 58 were polychaetes, 15 were mollusks, 27 were crustaceans, 3 were echinoderms and 13 were other groups. The average abundance and biomass of macrobenthos were 872.6 ind · m(-2) and 9.37 g · M(-2), respectively. By IRI index, Mediomastus sp., Helice sheni, Nemertinea and Neanthes sp. were ranked as the top 4 dominant species in the study area. Average Margalef's species richness diversity (d), Shannon diversity (H) and Pielou's evenness index (J) of macrobenthos were 2.119, 2.384 and 0.608, respectively, indicating slight pollution in the study area. Based on 30% similarity level, 8 transects could be grouped into 3 different communities. Compared with other intertidal zones in similar latitude, macrobenthos of Rushan Bay intertidal zone were characterized by higher species number, smaller body size and higher abundance. Besides the macrobenthic community structure and diversities, more exhaustive studies were needed to reveal the possible influence of shellfish culture on intertidal macrobenthic community.

Label-free quantitative proteomics analysis of dormant terminal buds of poplar.

Induction and break of bud dormancy are important features for perennial plants surviving extreme seasonal variations in climate. However, the molecular mechanism of the dormancy regulation, still remain poorly understood. To better understand the molecular basis of poplar bud dormancy, we used a label-free quantitative proteomics method based on nanoscale ultra performance liquid chromatography-ESI-MS(E) for investigation of differential protein expression during dormancy induction, dormancy, and dormancy break in apical buds of poplar (Populus simonii × P. nigra). Among these identified over 300 proteins during poplar bud dormancy, there are 74 significantly altered proteins, most of which involved in carbohydrate metabolism (22 %), redox regulation (19 %), amino acid transport and metabolism (10 %), and stress response (8 %). Thirty-one of these proteins were up-regulated, five were down-regulated during three phase, and thirty-eight were expressed specifically under different conditions. Pathway analysis suggests that there are still the presence of various physiological activities and a particular influence on photosynthesis and energy metabolism during poplar bud dormancy. Differential expression patterns were identified for key enzymes involved in major metabolic pathways such as glycolysis and the pentose phosphate pathway, thus manifesting the interplay of intricate molecular events in energy generation for new protein synthesis in the dormant buds. Furthermore, there are significant changes present in redox regulation and defense response proteins, for instance in peroxidase and ascorbate peroxidase. Overall, this study provides a better understanding of the possible regulation mechanisms during poplar bud dormancy.

Identification and analysis of the acetylated status of poplar proteins reveals analogous N-terminal protein processing mechanisms with other eukaryotes.

BACKGROUND: The N-terminal protein processing mechanism (NPM) including N-terminal Met excision (NME) and N-terminal acetylation (N(α)-acetylation) represents a common protein co-translational process of some eukaryotes. However, this NPM occurred in woody plants yet remains unknown. METHODOLOGY/PRINCIPAL FINDINGS: To reveal the NPM in poplar, we investigated the N(α)-acetylation status of poplar proteins during dormancy by combining tandem mass spectrometry with TiO2 enrichment of acetylated peptides. We identified 58 N-terminally acetylated (N(α)-acetylated) proteins. Most proteins (47, >81%) are subjected to N(α)-acetylation following the N-terminal removal of Met, indicating that N(α)-acetylation and NME represent a common NPM of poplar proteins. Furthermore, we confirm that poplar shares the analogous NME and N(α)-acetylation (NPM) to other eukaryotes according to analysis of N-terminal features of these acetylated proteins combined with genome-wide identification of the involving methionine aminopeptidases (MAPs) and N-terminal acetyltransferase (Nat) enzymes in poplar. The N(α)-acetylated reactions and the involving enzymes of these poplar proteins are also identified based on those of yeast and human, as well as the subcellular location information of these poplar proteins. CONCLUSIONS/SIGNIFICANCE: This study represents the first extensive investigation of N(α)-acetylation events in woody plants, the results of which will provide useful resources for future unraveling the regulatory mechanisms of N(α)-acetylation of proteins in poplar.

Genome-wide identification and in silico analysis of poplar peptide deformylases.

Peptide deformylases (PDF) behave as monomeric metal cation hydrolases for the removal of the N-formyl group (Fo). This is an essential step in the N-terminal Met excision (NME) that occurs in these proteins from eukaryotic mitochondria or chloroplasts. Although PDFs have been identified and their structure and function have been characterized in several herbaceous species, it remains as yet unexplored in poplar. Here, we report on the first identification of two genes (PtrPDF1A and PtrPDF1B) respectively encoding two putative PDF polypeptides in Populus trichocarpa by genome-wide investigation. One of them (XP_002300047.1) encoded by PtrPDF1B (XM_002300011.1) was truncated, and then revised into a complete sequence based on its ESTs support with high confidence. We document that the two PDF1s of Populus are evolutionarily divergent, likely as a result of independent duplicated events. Furthermore, in silico simulations demonstrated that PtrPDF1A and PtrPDF1B should act as similar PDF catalytic activities to their corresponding PDF orthologs in Arabidopsis. This result would be value of for further assessment of their biological activities in poplar, and further experiments are now required to confirm them.

Asymmetrical distribution of antennal sensilla in the female Anastatus japonicus Ashmead (Hymenoptera: Eupelmidae).

Anastatus japonicus Ashmead (Hymenoptera: Eupelmidae) is an important egg parasitoid of several major insect pests. To better understand its host finding mechanisms, the antennal sensilla of female wasp were investigated by scanning electron microscopy. Sensilla chaetica were found mainly on radicle and pedicel segments of the antennae. i-Type sensilla, s. campaniformia, and corneous sensilla were detected on the leeward side, while s. coeloconica and lance sensilla were presented on the windward side of the antennae. S. trichodea and s. basiconica were more abundant on the leeward side than on the windward side of the antennae. More s. placodea were found on the windward side than on the leeward side of the right antenna, while the opposite results were observed on the left antenna. Overall, more s. placodea were found on the right antenna than that on the left antenna. The numbers of s. trichodea and s. basiconica on the clava or the third flagellum antennomere of the right antenna were more than those of the left antenna, whereas their distribution patterns on the other corresponding antennomeres were reverse. Our results showed that there is a strong asymmetrical antennal sensilla distribution quantitatively and spatially between the left and right antennae. Placoid sensilla are present more on the right antenna than on the left antenna. S. campaniformia, corneous sensilla, and i-type sensilla were found only on the leeward side of the antennal clava, while their external morphology and potential functions were described and discussed in detail for the first time.

A glycine-rich RNA-binding protein can mediate physiological responses in transgenic plants under salt stress.

Glycine-rich RNA-binding proteins (GRPs) are involved in post-transcriptional regulation of genes, which have been found to play a role in stress response. However, whether GRPs can mediate some physiological responses related to salt stress tolerance is still not known. In the present study, we investigated the role of GRPs in salt stress-induced physiological responses by generating transgenic tobacco lines overexpressing a GRP (LbGRP1) gene from Limonium bicolor (Bunge) Kuntze. Compared with wild type (WT) tobacco, the transgenic plants showed significantly improved superoxide dismutase and catalase activities under salt stress conditions. Levels of proline in the transgenic plants were significantly higher than those in the WT plants grown under NaCl stress conditions. Furthermore, Na(+) content and Na(+)/K(+) ratio in the transgenic plants were lower than those in the WT plants under both normal growth and stress conditions. These results suggested that overexpression of the LbGRP1 gene can affect some physiological processes associated with salt tolerance of plants. Therefore, we hypothesize that LbGST1 can enhance stress resistance by mediating some physiological pathways.

Identification and analysis of phosphorylation status of proteins in dormant terminal buds of poplar.

BACKGROUND: Although there has been considerable progress made towards understanding the molecular mechanisms of bud dormancy, the roles of protein phosphorylation in the process of dormancy regulation in woody plants remain unclear. RESULTS: We used mass spectrometry combined with TiO2 phosphopeptide-enrichment strategies to investigate the phosphoproteome of dormant terminal buds (DTBs) in poplar (Populus simonii × P. nigra). There were 161 unique phosphorylated sites in 161 phosphopeptides from 151 proteins; 141 proteins have orthologs in Arabidopsis, and 10 proteins are unique to poplar. Only 34 sites in proteins in poplar did not match well with the equivalent phosphorylation sites of their orthologs in Arabidopsis, indicating that regulatory mechanisms are well conserved between poplar and Arabidopsis. Further functional classifications showed that most of these phosphoproteins were involved in binding and catalytic activity. Extraction of the phosphorylation motif using Motif-X indicated that proline-directed kinases are a major kinase group involved in protein phosphorylation in dormant poplar tissues. CONCLUSIONS: This study provides evidence about the significance of protein phosphorylation during dormancy, and will be useful for similar studies on other woody plants.

Comparative temporal analyses of the Pinus sylvestris L. var. mongolica litv. apical bud proteome from dormancy to growth.

Bud dormancy in perennial plants adapts to environmental and seasonal changes. Bud dormancy is of ecological interest because it affects forest population growth characteristics and is of economical interest because it impacts wood production levels. To understand Pinus sylvestris L. var. mongolica litv. bud-dormancy and bud-burst mechanisms, we characterized the proteomes of their apical buds at the four critical stages that occur during the dormancy-to-growth transition. Ninety-six proteins with altered expression patterns were identified using NanoLC-ESI-MS/MS. The majority of these proteins (57%) are involved in metabolic and other cellular processes. For 28% of the proteins, a function could not be assigned. However, because their expression levels changed, they may be potential candidate bud development- or dormancy-related proteins. Of the 75 non-redundant bud proteins identified, ascorbate peroxidase, pathogenesis-related protein PR-10, and heat shock proteins dramatically increased during August and November, suggesting that they may involved in the initiation of bud dormancy. Conversely, S-adenosylmethionine synthetase, abscisic acid/stress-induced proteins, superoxide dismutase (SOD), caffeoyl-CoA O-methyltransferase, actin, and type IIIa membrane protein cp-wap13 had greater expression levels during April, suggesting that they may be involved in the initiation of bud dormancy-release. Cell division cycle protein 48 and eukaryotic initiation factors 4A-15 and 4A had greater expression levels during May, suggesting that they may regulate cell proliferate and differentiation in the shoot apical meristem. These observations provide insights into the molecular mechanisms that induce or break bud dormancy.

A systemic proteomic analysis of Populus chloroplast by using shotgun method.

The chloroplast is one of the most important organelles in plants. Proteomic investigations of chloroplasts have been undertaken for many herb plant species, but to date no such investigation has been reported for woody plant chloroplasts. In the present study we initiated a systematic proteomic study of Populus chloroplasts using a shotgun proteomic method. After isolation of chloroplasts and tryptic digestion of the proteins, the protein fragments were separated via HPLC using an SCX column, and the peptides were analyzed by LC-MS/MS; 119 proteins were successfully identified. Based on annotation information in the UniProtKB/Swiss-Prot database, these proteins were identified as being localized in the chloroplast thylakoid membrane, chloroplast stroma, chloroplast thylakoid lumen, and plastoglobules. Over 50% of all identified proteins were confirmed as chloroplast thylakoid proteins, and 85 are encoded by the chloroplast genome with the remaining proteins encoded by the nuclear genome. Based on functional annotation, these proteins were classified into four functional categories, including photosynthesis, redox regulation and stress, primary and secondary metabolism, transport and signaling. These data provide a valuable basis for further studies on photosynthesis in poplar species.

Cloning, heterologous expression, and functional characterization of a chitinase gene, Lbchi32, from Limonium bicolor.

In the present study, an endochitinase gene, Lbchi32, was cloned from Limonium bicolor. The cDNA sequence of Lbchi32 was 1,443 bp in length and encoded 319 amino acid residues. The DNA sequence of Lbchi32 was 2,512 bp in length and contained three exons and two introns. The Lbchi32 gene was inserted into a pPIC9 vector and transferred into Pichia pastoris strains GS115 and KM71 for heterologous expression. SDS-PAGE analyses indicated that LbCHI32 was expressed in both GS115 and KM71 and that it was secreted extracellularly. The optimal reaction conditions for LbCHI32 activity are 45 degrees C, pH 5.0, and 5 mM Ba(2+). The LbCHI32 enzyme can efficiently degrade chitin, chitin derivatives, and the cell walls of different pathogenic fungi, including phytopathogenic Rhizoctonia solani, Fusarium oxysporum, Sclerotinia sclerotiorum, Valsa sordida, Septoria tritici, and Phytophthora sojae. These findings suggest that Lbchi32 has potential use in the degradation of chitin and chitin derivatives.

[Cloning and stress tolerance analysis of an LbGRP gene in Limonium bicolor].

Glycine-rich RNA-binding proteins (GRP) are involved in post-transcriptional regulation, and play important roles in plant growth, development and stress response. In the present study, the full-length cDNA of a GRP gene (LbGRP, GenBank accession number: GQ398238) was cloned from a cDNA library of Limonium bicolor. To investigate the stress tolerance of LbGRP, the recombinant plasmid pYES2-LbGRP was constructed by inserting the LbGRP gene into the yeast expression vector pYES2. The recombinant plasmid pYES2-LbGRP was transformed into yeast Saccharomyces cerevisiae INVSc1, and the INVSc1 strain transformed with empty pYES2 was used as the control. The recombinant yeast INVSc1 harboring LbGRP (pYES2-LbGRP) and the control INVSc1 harboring empty pYES2 were treated with NaCl, KCl, NaHCO3, Na2CO3, drought and frezzing, respectively, and their survial rates were compared under these stress conditions. The results showed that the survival rates of the recombinant yeast INVScl (pYES2-LbGRP) were higher than that of the control strain under these stress conditions, indicating that the LbGRP is tolerant to NaCl, KCl, NaHCO3, Na2CO3, drought and frezzing stresses. These results suggested that LbGRP plays a role in stress tolerance of L. bicolor.

Phosphoproteomic identification and phylogenetic analysis of ribosomal P-proteins in Populus dormant terminal buds.

To better understand the role that reversible phosphorylation plays in woody plant ribosomal P-protein function, we initiated a phosphoproteomic investigation of P-proteins from Populus dormant terminal buds. Using gel-free (in-solution) protein digestion and phosphopeptide enrichment combined with a nanoUPLC-ESI-MS/MS strategy, we identified six phosphorylation sites on eight P-proteins from Populus dormant terminal buds. Among these, six Ser sites and one Thr site were identified in the highly conserved C-terminal region of eight P-proteins of various P-protein subfamilies, including two P0, two P1, three P2 and one P3 protein. Among these, the Thr site was shown to be novel and has not been identified in any other organisms. Sequence analysis indicated that the phosphothreonine sites identified in the C-terminus of Ptr RPP2A exclusively occurred in woody species of Populus, etc. The identified phosphopeptides shared a common phosphorylation motif of (S/T)XX(D/E) and may be phosphorylated in vivo by casein kinase 2 as suggested by using Scansite analysis. Furthermore, phylogenetic analysis suggested that divergence of P2 also occurred in Populus, including type I and type II. To the best of our knowledge, this is the first systematic phosphoproteomic and phylogenetic analysis of P-proteins in woody plants, the results of which will provide a wealth of resources for future understanding and unraveling of the regulatory mechanisms of Populus P-protein phosphorylation during the maintenance of dormancy.

Cloning and characterization of a chitinase gene Lbchi31 from Limonium bicolor and identification of its biological activity.

Chitinases are digestive enzymes that break down glycosidic bonds in chitin. In the current study, an endochitinase gene Lbchi31 was cloned from Limonium bicolor. The cDNA sequence of Lbchi31 was 1,107 bp in length, encoding 322 amino acid residues with a calculated molecular mass of 31.7 kDa. Clustal analysis showed that there was a highly conserved chitin-binding domains in Lbchi31 protein, containing four sulfide bridges. The Lbchi31 gene was inserted into the pPIC9 vector and transferred into yeast Pichia pastoris GS115 and KM71 for heterologous expression. The transformant harboring the Lbchi31 gene showed a clearly visible protein band with a molecular mass of more than 31 kDa in the SDS-PAGE gel, indicating that it had been translated in P. pastoris. Enzyme characterization showed that the optimal reaction condition for chitinase LbCHI31 activity was: 40 degrees C, pH of 5.0 and 5 mmol l(-1) of Mn(2+). The maximum enzyme activity was 0.88 U ml(-1) following exposure to the cell wall chitin of Valsa sordida. The LbCHI31 enzyme can efficiently degrade cell wall chitin of the phytopathogenic Rhizoctonia solani, Fusarium oxysporum, Sclerotinia sclerotiorum, V. sordida, Septoria tritici and Phytophthora sojae, suggesting that it has the biocontrol function to fungal phytopathogen.

Enhanced salt tolerance of transgenic poplar plants expressing a manganese superoxide dismutase from Tamarix androssowii.

Superoxide dismutases (SODs) play important role in stress tolerance of plants. In this study, an MnSOD gene (TaMnSOD) from Tamarix androssowii, under the control of the CaMV35S promoter, was introduced into poplar (Populus davidiana x P. bolleana). The physiological parameters, including SOD activity, malondialdehyde (MDA) content, relative electrical conductivity (REC) and relative weight gain, of transgenic lines and wild type (WT) plants, were measured and compared. The results showed that SOD activity was enhanced in transgenic plants, and the MDA content and REC were significantly decreased compared to WT plants when exposed to NaCl stress. In addition, the relative weight gains of the transgenic plants were 8- to 23-fold of those observed for WT plants after NaCl stress for 30 days. The data showed that the SOD activities that increased in transgenic lines are 1.3-4-folds of that increased in the WT plant when exposed to NaCl stress. Our analysis showed that increases in SOD activities as low as 0.15-fold can also significantly enhance salt tolerance in transgenic plants, suggesting an important role of increased SOD activity in plant salt tolerance

Identification of low abundance polyA-binding proteins in Arabidopsis chloroplast using polyA-affinity column.

Proteins could be well separated and further identified by the use of 2-DE and related techniques. Yet, there are many proteins could not be detected even by more effective dyes because of their inherent low abundance or their low resolution. As a result, polyA-affinity column was used as a method to enrich polyA-binding proteins and then identified by MALDI-TOF-MS. In this study, 23 Arabidopsis chloroplast protein spots coded by 18 genes were identified, and majority of these proteins were classified into three related categories according to their annotations in the Swiss-Prot database, including NAD-, RNA-, and ATP-binding motifs, respectively. The major goal of the present Arabidopsis chloroplast proteomics project was to identify novel polyA-binding proteins or protein isoforms located in Arabidopsis chloroplasts and the specific research of cellular proteins with extremely low transcription levels could be fulfilled.

ThPOD3, a truncated polypeptide from Tamarix hispida, conferred drought tolerance in Escherichia coli.

The ThPOD1 gene encodes a peroxidase and was isolated from a Tamarix hispida NaCl-stress root cDNA library. We found that ThPOD1 expression could be induced by abiotic stresses such as cold, salt, drought and exogenous abscisic acid. These findings suggested that ThPOD1 might be involved in the plant response to environmental stresses and ABA treatment. To elucidate the function of this gene, recombinant plasmids expressing full-length ThPOD1 as well as ThPOD2 (aa 41-337), and ThPOD3 (aa 73-337) truncated polypeptides were constructed. SDS-PAGE and Western blot analyses of the fusion proteins revealed that the molecular weights of ThPOD1, ThPOD2 and ThPOD3 were approximately 57, approximately 50 and approximately 47 kDa, respectively. Stress assays of E. coli treated with the recombinant plasmids indicated that ThPOD3 could improve resistance to drought stress. This finding could potentially be used to improve plant tolerance to drought stress via gene transfer.