[The regulatory roles of small RNAs in phytohormone signaling pathways].

Phytohormones are signaling molecules that control plant growth and development. Recent studies revealed that non-coding small RNAs play critical roles in plant development and stress responses via phytohormone signaling pathways. In this review, we summarize the present knowledge on the microRNAs (miRNAs) and secondary short interfering RNAs (siRNAs) involved in phytohormone signaling pathways, which include auxin, gibberellic acid, brassinosteroid and abscisic acid pathways. We also discuss their possible implications in phytohormone crosstalk during specific developmental processes.

Rapid construction of multiple sgRNA vectors and knockout of the Arabidopsis IAA2 gene using the CRISPR/Cas9 genomic editing technology.

IAA2 is a member of the Aux/IAA auxin responsive gene family in Arabidopsis thaliana. No iaa2 mutant has been reported until now, thus hindering its further mechanistic investigations. The normal genomic editing technology of CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) uses only a single guide RNA (sgRNA) to target one site in a specific gene, and the gene knockout efficiency is not high. Instead, multiple sgRNAs can target multiple sites; therefore, the efficiency may be improved. In the present investigation, we used the golden-gate cloning strategy and two rounds of PCR reactions to combine three sgRNAs in the same entry vector. The final expression vector was obtained by LR reactions with the destination vector containing the Cas9 expression cassette. Four out of the six sgRNAs were effective, and we also obtained a lot of insertion and deletion mutations. Compared with one sgRNA approach, multiple sgRNAs displayed higher gene-knockout efficiency and produced more germ-line mutants. Thus, we established a more rapid and efficient method and generated five mutants for further studies of IAA2 functions.

Progress on the autophagic regulators and receptors in plants.

Autophagy is an evolutionarily highly conserved catabolic pathway among eukaryotic cells that protects the organisms against environmental stress. Normally, autophagy is mainly involved with autophagy-related proteins(ATGs) and autophagic regulators including a series of cytoplasmic proteins and small molecules. Besides, the selective autophagy, which targets damaged organalles or protein aggregates, is mediated by the additional receptors to help the ATGs recognize different substrates. In this review, we summarize recent advances in autophagic regulators like ROS(Reactive oxygen species), TOR(Target of rapamycin) and receptors like NBR1(Neighbor of BRCA1 gene protein), RPN10(Regulatory particle non-ATPase 10) as well as their functional mechanisms mainly in Arabidopsis thaliana.

Association of specific pectin methylesterases with Al-induced root elongation inhibition in rice.

The negative charges of cell wall pectin molecules attributed by pectin methylesterase (PME, EC 3.1.1.11) contribute to Al binding capacity. We examined the expression profiles of 35 members of the PME gene family in the root apex of an Al-sensitive rice 'Zhefu802' under Al stress. While root elongation was inhibited by 40% after 3-h exposure to 25 µM Al, cell wall PME activity and the abundance of eight PME genes transcripts were increased. The same Al treatment which had almost no effect on root elongation of an Al-resistant rice ssp. japonica 'Nipponbare' did not change the expression patterns of these eight PME genes. However, when Al concentration was increased to 50 µM, by which the root elongation of 'Nipponbare' was inhibited by 40% too, the expression of these PME genes were also upregulated except two genes with no signal. These suggest a possible correlation between the upregulated genes and Al-induced inhibition of root elongation in rice. Furthermore, these eight PME genes behaved differently when subjected to CdCl2 and LaCl3 treatments, implying the specificity of different PME genes in response to different metal toxicities. The transgenic rice overexpressing one of these eight PME genes OsPME14 showed higher PME activity and Al content in root tip cell wall, and became more sensitive to Al stress, verifying the involvement of the specific PME gene in Al toxicity. Therefore, our results provided the molecular evidence to connect the expression of specific PME genes with the Al-induced inhibition of root elongation in rice.

[Recent advances in the techniques of protein-protein interaction study].

Protein-protein interactions play key roles in the development of organisms and the response to biotic and abiotic stresses. Several wet-lab methods have been developed to study this challenging area,including yeast two-hybrid system, tandem affinity purification, Co-immunoprecipitation, GST Pull-down, bimolecular fluorescence complementation, fluorescence resonance energy transfer and surface plasmon resonance analysis. In this review, we discuss theoretical principles and relative advantages and disvantages of these techniques,with an emphasis on recent advances to compensate for limitations.

De novo characterization of the Chinese fir (Cunninghamia lanceolata) transcriptome and analysis of candidate genes involved in cellulose and lignin biosynthesis.

BACKGROUND: Chinese fir (Cunninghamia lanceolata) is an important timber species that accounts for 20-30% of the total commercial timber production in China. However, the available genomic information of Chinese fir is limited, and this severely encumbers functional genomic analysis and molecular breeding in Chinese fir. Recently, major advances in transcriptome sequencing have provided fast and cost-effective approaches to generate large expression datasets that have proven to be powerful tools to profile the transcriptomes of non-model organisms with undetermined genomes. RESULTS: In this study, the transcriptomes of nine tissues from Chinese fir were analyzed using the Illumina HiSeq™ 2000 sequencing platform. Approximately 40 million paired-end reads were obtained, generating 3.62 gigabase pairs of sequencing data. These reads were assembled into 83,248 unique sequences (i.e. Unigenes) with an average length of 449 bp, amounting to 37.40 Mb. A total of 73,779 Unigenes were supported by more than 5 reads, 42,663 (57.83%) had homologs in the NCBI non-redundant and Swiss-Prot protein databases, corresponding to 27,224 unique protein entries. Of these Unigenes, 16,750 were assigned to Gene Ontology classes, and 14,877 were clustered into orthologous groups. A total of 21,689 (29.40%) were mapped to 119 pathways by BLAST comparison against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The majority of the genes encoding the enzymes in the biosynthetic pathways of cellulose and lignin were identified in the Unigene dataset by targeted searches of their annotations. And a number of candidate Chinese fir genes in the two metabolic pathways were discovered firstly. Eighteen genes related to cellulose and lignin biosynthesis were cloned for experimental validating of transcriptome data. Overall 49 Unigenes, covering different regions of these selected genes, were found by alignment. Their expression patterns in different tissues were analyzed by qRT-PCR to explore their putative functions. CONCLUSIONS: A substantial fraction of transcript sequences was obtained from the deep sequencing of Chinese fir. The assembled Unigene dataset was used to discover candidate genes of cellulose and lignin biosynthesis. This transcriptome dataset will provide a comprehensive sequence resource for molecular genetics research of C. lanceolata.

[Recent research progress of biogenesis and functions of miRNA*].

MicroRNA*s are about 22nt noncoding RNAs, which are processed from precursors with a characteristic hairpin secondary structure in the biogenesis of microRNAs. Recently, miRNA* strands were shown to mediate post-transcriptional regulatory networks, rather than serve merely as non-functional by-product in general view. Unlike miRNAs bound to AGO1, miRNA* strands are bound to AGO2 to form RISC duplex to mediate RNAi, which is similar to siRNA. This paper mainly reviewed the recent research progresses on miRNA*, such as the biosynthesis, biological characteristics, and functions.

Regulation of auxin response by miR393-targeted transport inhibitor response protein 1 is involved in normal development in Arabidopsis.

miR393, which is encoded by MIR393a and MIR393b in Arabidopsis, post-transcriptionally regulates mRNAs for the F-box auxin receptors TIR1 (Transport Inhibitor Response Protein 1), AFB1 (Auxin Signaling F-box Protein 1), AFB2 and AFB3. However, biological functions of the miR393-TIR1/AFBs module in auxin response and plant development is not fully understood. In the study herein, we demonstrate that miR393 accumulated in response to exogenous IAA treatment, and its induction was due to enhanced MIR393b transcription but not MIR393a. Overexpression of a miR393-resistant form of TIR1 (mTIR1) enhanced auxin sensitivity and led to pleiotropic effects on plant development including inhibition of primary root growth, overproduction of lateral roots, altered leave phenotype and delayed flowering. Furthermore, miR393 level was increased in 35S:mTIR1 plant, suggesting that TIR1 promoted the expression of miR393 by a feedback loop. The interaction between miR393 and its target indicates a fine adjustment to the roles of the miR393-TIR1 module, which is required for auxin responses in plant development.

Identification and characterization of two bamboo (Phyllostachys praecox) AP1/SQUA-like MADS-box genes during floral transition.

Bamboo (Bambusoideae) is by far the largest member of the grass family Poaceae, which is vital to the economy of many countries in the tropics and subtropics. However, the mechanism of flowering of bamboo (Phyllostachys praecox) is still unknown. In this study, we isolated two novel genes from P. praecox and evaluated their functional characteristics. The sequence and phylogenetic analysis indicated that these two genes, named PpMADS1 and PpMADS2, belong to FUL3 and FUL1 clade of Poaceae AP1/SQUA-like genes, respectively. The PpMADS2 possesses a truncated C terminus lacking the highly conserved paleoAP1 motif. It was further confirmed that the truncated C-terminal region was produced by natural sequence deletion in exons, but not by alternative splicing. Ectopic expression of PpMADS1 and PpMADS2 significantly promoted early flowering through upregulation of AP1 in Arabidopsis. Yeast two-hybrid experiments demonstrated that AP1 protein can interact with PpMADS1 but not PpMADS2, suggesting that these two genes may act differently in signaling early flowering of bamboo plants. RT-qPCR and in situ hybridization analysis revealed distinct expression patterns of these two genes in vegetative and reproductive tissues of bamboo. Taken together, our results suggest that both PpMADS1 and PpMADS2 are involved in floral transition, and PpMADS2 might play more important roles than PpMADS1 in floral development of Phyllostachys praecox.

Regulation of flowering time via miR172-mediated APETALA2-like expression in ornamental gloxinia (Sinningia speciosa).

We investigated the microRNA172 (miR172)-mediated regulatory network for the perception of changes in external and endogenous signals to identify a universally applicable floral regulation system in ornamental plants, manipulation of which could be economically beneficial. Transgenic gloxinia plants, in which miR172 was either overexpressed or suppressed, were generated using Agrobacterium-mediated transformation. They were used to study the effect of altering the expression of this miRNA on time of flowering and to identify its mRNA target. Early or late flowering was observed in transgenic plants in which miR172 was overexpressed or suppressed, respectively. A full-length complementary DNA (cDNA) of gloxinia (Sinningia speciosa) APETALA2-like (SsAP2-like) was identified as a target of miR172. The altered expression levels of miR172 caused up- or down-regulation of SsAP2-like during flower development, which affected the time of flowering. Quantitative real-time reverse transcription PCR analysis of different gloxinia tissues revealed that the accumulation of SsAP2-like was negatively correlated with the expression of miR172a, whereas the expression pattern of miR172a was negatively correlated with that of miR156a. Our results suggest that transgenic manipulation of miR172 could be used as a universal strategy for regulating time of flowering in ornamental plants.

Molecular cloning, expression analyses and primary evolution studies of REV- and TB1-like genes in bamboo.

Most cultured bamboos are perennial woody evergreens that reproduce from rhizomes. It is unclear why some rhizome buds develop into aerial bamboo shoots instead of new rhizomes. REVOLUTA (REV)-like Class III homeodomain leucine-zipper (HD-Zip) proteins and TEOSINTE BRANCHED1 (TB1)-like transcription factors have been shown to play regulatory roles in meristem initiation and outgrowth. We cloned and analyzed the bamboo (Phyllostachys praecox C.D. Chu & C.S. Chao.) REV- (PpHB1) and TB1-like (PpTB1) gene. Gene expression was mainly detected by in situ hybridization. PpHB1 expression was detected in the tips of lateral buds, on the adaxial portion of the leaf and within the developing procambium, indicating its close correlation to rhizome bud formation and procambial development. PpTB1 expression was mainly detected on the top of buds at later developmental stages, suggesting it was more likely involved in bud outgrowth. Meristem genes might therefore serve as specific molecular markers of rhizome bud development and could be useful in studies designed to elucidate the mechanisms underlying bamboo shoot development. In addition, meristem genes such as TB1-like sequences may be useful in phylogenetic analyses of bamboo species.

Inhibition of growth and development of root border cells in wheat by Al.

The production and development of border cells vary with genotype, and they are released in wheat at an earlier stage of root development than other species studied so far. No significant difference was observed in the maximum number of border cells between Al-tolerant (Atlas 66) and Al-sensitive (Scout 66) cultivars in the absence of Al treatment. Al seriously inhibited the production and release of border cells, resulting in clumping of border cells in Scout 66, but less clustering in Atlas 66. The number of border cells released from roots treated with Al is significantly less than that from roots grown without Al treatment. Al treatment induced the death of detached border cells in vitro and they were killed by a 20-h treatment with 25 micro m Al. No significant difference in survival percentage of detached border cells was observed between Atlas 66 and Scout 66, regardless of the presence or absence of Al. The removal of border cells from root tips of both Atlas 66 and Scout 66 enhanced the Al-induced inhibition of root elongation concomitant with increased Al accumulation in the root. These results suggest that border cells adhered to the root tips play a potential role in the protection of root from Al injury in wheat.

cDNA cloning of growth hormone from giant panda (Ailuropoda melanoleuca) and its expression in Escherichia coli.

A cDNA encoding Ailuropoda melanoleuca growth hormone (AmGH) was isolated from pituitary total RNA using RT-PCR and expressed in Escherichia coli. This is the first report of a GH nucleotide and amino acid (aa) sequence from giant panda. The open reading frame of AmGH (651 bp) encodes a precursor of 216 aa comprising a 26 aa signal peptide and a 190 aa mature protein with four cysteine residues similar to the typical primary structure of mammalian GH precursor. AmGH shares a high degree of identity (54-98.9%) with that of mammals, birds and amphibians, but a very low identity with bony fish GH (only 20-30%). The mature AmGH exhibits striking similarity to that of putative ancestral GH with a difference of only two residues, indicating a very slow basal rate of molecular evolution. The DNA fragment encoding mature AmGH was then subcloned into the pGEX-4T-1 expression vector and highly expressed in E. coli host BL21 with IPTG induction. The expressed proteins fused to GST were found to be sequestered into inclusion bodies and therefore the NaOH method was employed to solubilize the inclusion bodies; the proteins were further purified by Glutathione Sepharose 4B affinity chromatography. The production and purification of GST-AmGH reported here provide a basis for further studies on the biological activity of AmGH.

Cloning and sequence analysis of FSH and LH in the giant panda (Ailuropoda melanoleuca).

The giant panda (Ailuropoda melanoleuca) is an endangered species and indigenous to China. It has been proposed that it has a highly specialized reproductive pattern with low fecundity, but little is known about its basic reproductive biology at the molecular level. In this report the genes encoding gonadotropin subunits alpha, follicle-stimulating hormone (FSH) beta and luteinizing hormone (LH) beta of the giant panda were amplified for the first time by RT-PCR from pituitary total RNA, and were cloned, sequenced and analyzed. The results revealed that the open reading region (ORF) of gonadotropin subunits alpha, FSH beta and LH beta are 363, 390 and 426 bp long, respectively. They displayed a reasonably high degree (74-94, 85-93, 75-91%, for alpha, FSH beta and LH beta subunits, respectively) of identity when deduced amino acids were compared with homologous sequences from partial available mammals including human, cattle, sheep, pig, rat, mouse. Three distinct differences were found at the site of 59 aa of the alpha subunit and 55 aa, 68 aa of FSH beta subunit. Our results provide an insight into understanding the mechanism of reproduction regulation and genetic characteristics of giant panda which will make an actual contribution to its conservation. In addition they lay a foundation for a further study towards producing recombinant panda FSH and LH which can be used in artificial breeding aimed to increase its captive reproductive efficiency.

[Cloning and expression of pituitary prolactin gene in Ailuropoda melanoleuca].

The giant panda (Ailuropoda melanoleuca) is an endangered species and indigenous to China. It has been proposed that it has a highly specialized reproductive pattern with low fecundity, but little is known about its basic reproductive biology at molecular level. In this study,the pituitary prolactin (PRL) cDNA of giant panda was amplified by RT-PCR from pituitary total RNA and then cloned, sequenced and submitted to GenBank (GenBank accession No. AY161285). The sequence analysis revealed that the giant panda prolactin cDNA contains a 687-nucleotide open reading frame encoding the prolactin prohormone of 229 amino acid residues. The signal peptide contains 30 amino acid residues and the mature prolactin is composed of 199 amino acid residues. Then the DNA fragment amplified was subcloned into pGEX-4T-1 procaryotic expression plasmid and protein expression was induced by IPTG in Escherichia coil BL21. SDS-PAGE analysis revealed the PRL protein is infusible. The multiple sequence alignments revealed that the homology of giant panda is 95% to cat and pig, 80% - 70% to human, cow and goat, 52% to rat and 45.9% to mouse at the amino acid level. The 64th amino acid of giant panda prolactin is hydrophilic serine instead of hydrophobic proline of cat, goat, and cow or hydrophobic alanine of human.

[Expression of CFL gene during differentiation of floral and vegetative buds in cucumber cotyledonary nodes cultured in vitro].

CFL gene, a LFY homologue, was cloned from cucumber (Cucumis sativus L.). In this paper, in situ hybridization was performed to analyze the expression pattern of CFL gene at the stage of floral and vegetative buds differentiation in cucumber cotyledonary nodes cultured in vitro. The results showed that at the stage of floral differentiation, CFL gene was strongly expressed in primordia, floral organ primordia, and each whirl of floral organs at the early stage of their formation, but weakly expressed or not expressed in floral organs after their formation (Fig. 2). At the stage of vegetative bud differentiation, CFL gene was strongly expressed in meristem, leaf primordium and young leaves, and no apparent expression signal was detected in mature tissues (Fig. 3). The results suggest that the expression of CFL gene be necessary for the differentiation and formation of floral and vegetative primordias, and it plays an important role in floral and vegetative development in cucumber. The results also indicate that CFL gene involving in mitosis initiation, mitosis controlling, and transformation of vegetative meristem to floral meristem.

[The application of transgenic plant in evaluating the genotoxicity of environmental contaminants].

Environmental contaminants are powerful mutagenic factors for organisms. Several testing materials and methods have been used to assess the genotoxicity of environmental factors. Transgenic plants testing system can not only evaluate the level of genotoxicity, but also provide information on the genetic effects at molecular level. We introduce the use of transgenic plants in biomonitoring environmental factors.

[Environmental stress-induced programmed cell death in higher plants].

Programmed cell death (PCD) research in higher plants has blossomed in the past ten years. Many evidences suggested that reactive oxygen species,ethylene, Ca2+, salicylic acid, nitric oxide etc. are important signal molecules during environmental stress-induced PCD in plants. Like apoptosis in animals, there also exists a Caspase-dependent PCD signal transduction pathway, in which mitochondrion plays a role of central depot.

[Regulation network and biological roles of LEAFY in Arabidopsis thaliana in floral development].

Recent research progress on regulation network and biological roles of LFY gene in Arabidopsis thaliana and its homologue genes in floral development are reviewed emphatically in the present paper. LFY gene expresses widely in both vegetative and reproductive tissues in different higher plants, therefore investigation on role of LFY gene on flowering is of general significance. LFY gene plays an important role to promote flower formation by interaction and coordination with other genes,such as TFL, EMF, AP1, AP2, CAL, FWA, FT, AP3, PI, AG, UFO, CO, LD, GA1 etc, and a critical level of LFY expression is essential. LFY gene not only controls flowering-time and floral transition,but also plays an important role in inflorescence and floral organ development. It was situated at the central site in gene network of flowering regulation,positively or negatively regulates the level or activities of flowering-related genes. Some physiological factors, such as carbon sources, phytohormones, affect directly or indirectly the expression and actions of LFY gene. This indicates that level of LFY expression can also be regulated with physiological methods. It is probable that we can explain the principal mechanism of flowering by regulation network of LFY gene.

[Analysis of polymorphic RAPD fragments in P. Taiwanensis Hayata using an integrated microflluidic chip-based system].

Randomly amplified polymorphic DNA (RAPD) markers quickly provide linkage information, especially in conifers where haploid megagametophytes can be used for genotyping. Traditionally use of slab gel electrophresis results in qualitative data that can be manually manipulated to gain semiquantitative information about the polymorphic RAPD fragments. We have proposed the use of an integrated microfluidic chip-based system as a new tool in the analysis of polymorphic RAPD fragments. The chip-based method was found to be very sensitive,requiring much less sample and only quarter the time compared to the agarose gel method. The automated data analysis sizes and quantitates the DNA fragments, thus yielding a more thorough,reproducible, sensitive, and rapid analysis.