Yikun He

The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration

Significance The genome analysis presented here represents a major step forward in the field of desiccation tolerance and a much-anticipated resource that will have a far-reaching effect in many areas of plant biology and agriculture. We present the ∼1.69-Gb draft genome of Boea hygrometrica, an important plant model for understanding responses to dehydration. To our knowledge, this is the first genome sequence of a desiccation-tolerant extremophile, offering insight into the evolution of this important trait and a first look, to our knowledge, into the genome organization of desiccation tolerance. The underpinning genome architecture and response in relation to the hydration state of the plant and its role in the preservation of cellular integrity has important implications for developing drought tolerance improvement strategies for our crops. “Drying without dying” is an essential trait in land plant evolution. Unraveling how a unique group of angiosperms, the Resurrection Plants, survive desiccation of their leaves and roots has been hampered by the lack of a foundational genome perspective. Here we report the ∼1,691-Mb sequenced genome of Boea hygrometrica, an important resurrection plant model. The sequence revealed evidence for two historical genome-wide duplication events, a compliment of 49,374 protein-coding genes, 29.15% of which are unique (orphan) to Boea and 20% of which (9,888) significantly respond to desiccation at the transcript level. Expansion of early light-inducible protein (ELIP) and 5S rRNA genes highlights the importance of the protection of the photosynthetic apparatus during drying and the rapid resumption of protein synthesis in the resurrection capability of Boea. Transcriptome analysis reveals extensive alternative splicing of transcripts and a focus on cellular protection strategies. The lack of desiccation tolerance-specific genome organizational features suggests the resurrection phenotype evolved mainly by an alteration in the control of dehydration response genes.

Role of cytokinin and salicylic acid in plant growth at low temperatures

Low temperature restrains plant growth by inhibiting the cell cycle, and phytohormones play important roles in this case; however, the molecular mechanisms whereby phytohormones affect growth at low temperature are largely unknown. When grown at 23, 16, 10, and 4°C, we found that Arabidopsis thaliana could develop with normal morphology, but needed a prolonged period of cultivation. By screening mutants, we could implicate cytokinin and salicylic acid. At 4°C, both amp1 plants, which have an increased level of cytokinin, and wild-type plants treated with exogenous cytokinin, displayed relative growth rates greater than control by increasing total cell number. Additionally, transgenic NahG plants, which have lower salicylic acid content, grew faster than wild-type accompanied by larger cells. Expression of C-repeat binding transcription factors (CBFs), that mediate cold acclimation by stimulation of the expression of cold-inducible genes, was similar in all tested genotypes. Thus CBF expression did not correlate with the observed enhanced growth in mutants. The improved growth coincided with elevated expression of CYCD3;1, especially in NahG plants. At 4°C, enhanced endoreduplication took responsibility for larger cells in NahG plants, while enhanced cell division was observed in amp1 plants.

Transcriptome of Protoplasts Reprogrammed into Stem Cells in Physcomitrella patens

Background Differentiated plant cells can retain the capacity to be reprogrammed into pluripotent stem cells during regeneration. This capacity is associated with both cell cycle reactivation and acquisition of specific cellular characters. However, the molecular mechanisms underlying the reprogramming of protoplasts into stem cells remain largely unknown. Protoplasts of the moss Physcomitrella patens easily regenerate into protonema and therefore provide an ideal system to explore how differentiated cells can be reprogrammed to produce stem cells. Principal findings We obtained genome-wide digital gene expression tag profiles within the first three days of P. patens protoplast reprogramming. At four time-points during protoplast reprogramming, the transcript levels of 4827 genes changed more than four-fold and their expression correlated with the reprogramming phase. Gene ontology (GO) and pathway enrichment analysis of differentially expressed genes (DEGs) identified a set of significantly enriched GO terms and pathways, most of which were associated with photosynthesis, protein synthesis and stress responses. DEGs were grouped into six clusters that showed specific expression patterns using a K-means clustering algorithm. An investigation of function and expression patterns of genes identified a number of key candidate genes and pathways in early stages of protoplast reprogramming, which provided important clues to reveal the molecular mechanisms responsible for protoplast reprogramming. Conclusions We identified genes that show highly dynamic changes in expression during protoplast reprogramming into stem cells in P. patens. These genes are potential targets for further functional characterization and should be valuable for exploration of the mechanisms of stem cell reprogramming. In particular, our data provides evidence that protoplasts of P. patens are an ideal model system for elucidation of the molecular mechanisms underlying differentiated plant cell reprogramming.

The phosphoproteome in regenerating protoplasts from Physcomitrella patens protonemata shows changes paralleling postembryonic development in higher plants

Summary During protoplast regeneration, proteins related to cell morphogenesis, organogenesis and development adjustment were phosphorylated in Physcomitrella patens. These proteins play important roles in regulating postembryonic development in higher plants.

Chloroplast division is regulated by the circadian expression of FTSZ and MIN genes in Chlamydomonas reinhardtii

FTSZ and MIN proteins play important roles in plastid division. Having previously identified FTSZ genes in Chlamydomonas reinhardtii, we have now isolated the nucleus-encoded MIND and MINE1 genes from this species. Sequence analyses showed that MIND is highly conserved, while MINE1 is less well conserved. Both proteins were localized to chloroplasts, probably due to their N-terminal transit peptides. The transcription levels of FTSZ and MIN genes in synchronous cultures of C. reinhardtii, in which the chloroplasts divided synchronously with their host cells, were examined. Semi-quantitative reverse transcription PCR (RT-PCR) analyses showed that mRNA abundance displayed a circadian pattern under light-dark cycles and continuous light and dark conditions. Maximal mRNA levels correlated with cell division, and thus, chloroplast division. This work indicates that plastid division is regulated by the circadian expression of FTSZ and MIN genes.

Lignin reduction in transgenic poplars by expressing antisense CCoAOMT gene

Abstract The antisense Caffeoyl CoA O-methyltransferase (CCoAOMT) cDNA was transformed into Chinese white poplar (Populus tomentosa) mediated by Agrobacterium tumefaciens. Many factors affecting the transformation efficiency were studied and a stable transformation system was established. PCR-Southern blot analysis indicated that antisense CCoAOMT cDNA had been integrated into the genome of the transgenic poplars. RT-PCR and Western blot analyses demonstrated that the endogenous CCoAOMT gene was suppressed at both transcriptional and translational levels. Klason lignin content assay exhibited the lignin reduction to different degrees in transgenic poplars. The stems of partial transgenic poplars with the remarkable lignin reduction turned red, and the color distribution was stripped or spotted. Taken together, these results suggested that CCoAOMT gene would be a potential useful gene in altering lignin biosynthesis by biotechnology for improving wood properties.

ftsZ gene and plastid division

Plastid is one of the most important cellular organelles, the normal division process of plastid is essential for the differentiation and development of plant cells. For a long time, morphological observations and genetic analyses to special mutants are the major research fields of plastid division, but the molecular mechanisms underlying plastid division are largely unknown. Because of the endosymbiotic origin, plastid division might have mechanisms in common with those involved in bacterial cell division. It has been proved that several prokaryotic cell division genes also participate in the plastid division. Recently, the mechanisms of prokaryotic cell division have been well documented, which provides a valuable paradigm for understanding the plastid division mechanisms. In plants, the functional analyses offtsZ, a key gene involved both in bacteria and plastid division, have established the solid foundation for people to understand the plastid division in molecular level. In this paper we will make a review for the research history and progress of plastid division.

Tetrahydrofolate modulates Floral Transition through Epigenetic Silencing

Folate regulates DNA methylation to affect Arabidopsis flowering time. Folates, termed from tetrahydrofolate (THF) and its derivatives, function as coenzymes in one-carbon transfer reactions and play a central role in synthesis of nucleotides and amino acids. Dysfunction of cellular folate metabolism leads to serious defects in plant development; however, the molecular mechanisms of folate-mediated cellular modifications and physiological responses in plants are still largely unclear. Here, we reported that THF controls flowering time by adjusting DNA methylation-regulated gene expression in Arabidopsis (Arabidopsis thaliana). Wild-type seedlings supplied with THF as well as the high endogenous THF content mutant dihydrofolate synthetase folypoly-Glu synthetase homolog B exhibited significant up-regulation of the flowering repressor of Flowering Wageningen and thereby delaying floral transition in a dose-dependent manner. Genome-wide transcripts and DNA methylation profiling revealed that THF reduces DNA methylation so as to manipulate gene expression activity. Moreover, in accompaniment with elevated cellular ratios between monoglutamylated and polyglutamylated folates under increased THF levels, the content of S-adenosylhomo-Cys, a competitive inhibitor of methyltransferases, was obviously higher, indicating that enhanced THF accumulation may disturb cellular homeostasis of the concerted reactions between folate polyglutamylation and folate-dependent DNA methylation. In addition, we found that the loss-of-function mutant of CG DNA methyltransferase MET1 displayed much less responsiveness to THF-associated flowering time alteration. Taken together, our studies revealed a novel regulatory role of THF on epigenetic silencing, which will shed lights on the understanding of interrelations in folate homeostasis, epigenetic variation, and flowering control in plants.

Cloning and functional analysis of chloroplast division gene NtFtsZ2-l in Nicotiana tabacum

Abstract FtsZ protein plays an important role in the division of chloroplasts. With the finding and functional analysis of higher plant FtsZ proteins, people have deepened the understanding in the molecular mechanism of chloroplast division. Multiple ftsZ genes are diversified into two families in higher plants, ftsZl and ftsZ2. On the basis of the research on ftsZl family, we analyzed the function of NtFtsZ2-l gene in Nicotiana tabacum. Microscopic analysis of the sense and antisense NtFtsZ2-l transgenic tobacco plants revealed that the chloroplasts were abnormal in size and also in number when compared with wild-type tobacco chloroplasts. Our investigations confirmed that the NtFtsZ2-l gene is involved in plant chloroplast division.