Biomedical subjects

Kyung-Hwan Han

Publications and source records attributed to Kyung-Hwan Han.

14 recordsLinked to original sources

PubMed2006

Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana.

Our knowledge of the genetic control of wood formation (i.e., secondary growth) is limited. Here, we present a novel approach to unraveling the gene network regulating secondary xylem development in Arabidopsis, which incorporates complementary platforms of comparative-transcriptome analyses such as "digital northern" and "digital in situ" analysis. This approach effectively eliminated any genes that are expressed in either non-stem tissues/organs ("digital northern") or phloem and non-vascular regions ("digital in situ"), thereby identifying 52 genes that are upregulated only in the xylem cells of secondary growth tissues as "core xylem gene set". The proteins encoded by this gene set participate in signal transduction, transcriptional regulation, cell wall metabolism, and unknown functions. Five of the seven signal transduction-related genes represented in the core xylem gene set encode the essential components of ROP (Rho-related GTPase from plants) signaling cascade. Furthermore, the analysis of promoter sequences of the core xylem gene set identified a novel cis-regulatory element, ACAAAGAA. The functional significances of this gene set were verified by several independent experimental and bioinformatics methods.

Arabidopsis↗

PubMed2006

Loss of function of COBRA, a determinant of oriented cell expansion, invokes cellular defence responses in Arabidopsis thaliana.

An Arabidopsis T-DNA insertion mutant that results in complete loss-of-function of the COBRA gene has been identified. The COBRA gene encodes a putative glycosylphosphatidylinositol (GPI)-anchored protein that modulates cellulose deposition and oriented cell expansion in roots. The loss-of-function mutant allele (named "cob-5") exhibits abnormal cell growth throughout the entire plant body and accumulates massive amounts of stress response chemicals such as anthocyanins and callose. To gain further insight into the mechanism by which COBRA affects cell growth and physiology, the whole-genome gene expression profile of cob-5 plants was compared with that of wild-type plants. Consistent with the mutant phenotype, many genes involved in anthocyanin biosynthesis were up-regulated in the cob-5 plants, whereas genes involved in cell elongation were down-regulated. The most striking feature of the gene expression profile of cob-5 was the massive and co-ordinate induction of defence- and stress-related genes, many of which are regulated by the plant stress signal jasmonic acid (JA). Indeed, the cob-5 plants over-accumulated JA by nearly 8-fold compared with wild-type plants. Furthermore, induction of cell elongation defects in conditional allele cob-3 plants triggers the expression of a defence-responsive gene. These results provide potential clues to the mechanisms by which plant cells initially perceive biotic stress at the cell surface.

Arabidopsis↗

PubMed2006

Upregulation of an Arabidopsis RING-H2 gene, XERICO, confers drought tolerance through increased abscisic acid biosynthesis.

RING (really interesting new gene) zinc-finger proteins have important regulatory roles in the development of a variety of organisms. The XERICO gene encodes a small protein (162 amino acids) with an N-terminal trans-membrane domain and a RING-H2 zinc-finger motif located at the C-terminus. In silico gene-expression analysis indicated that XERICO is induced by salt and osmotic stress. Compared with wild-type (WT) Arabidopsis plants, transgenic plants overexpressing XERICO (35S::XERICO) exhibited hypersensitivity to salt and osmotic stress and exogenous abscisic acid (ABA) during germination and early seedling growth. When subjected to a drought treatment, transcriptional upregulation of a key ABA-biosynthesis gene, AtNCED3, was much faster and stronger in 35S::XERICO plants compared with WT plants. Further, upregulation of XERICO substantially increased cellular ABA levels. The adult 35S::XERICO plants, in contrast to early seedling growth, showed a marked increase in their tolerance to drought stress. Yeast two-hybrid screening indicated that XERICO interacts with an E2 ubiquitin-conjugating enzyme (AtUBC8) and ASK1-interacting F-box protein (AtTLP9), which is involved in the ABA-signaling pathway. Affymetrix GeneChip array analysis showed that the expressions of many of the genes involved in the biosynthesis of plant hormones (e.g. ethylene, brassinosteroid, gibberellic acid) were significantly changed in the 35S::XERICO plants. These results suggest that the homeostasis of various plant hormones might be altered in 35S::XERICO plants, possibly by overaccumulation of ABA.

Abscisic Acid↗

PubMed2006

Developmental and seasonal expression of PtaHB1, a Populus gene encoding a class III HD-Zip protein, is closely associated with secondary growth and inversely correlated with the level of microRNA (miR166).

In contrast to our knowledge of the shoot apical meristem, our understanding of cambium meristem differentiation and maintenance is limited. Class III homeodomain leucine-zipper (HD-Zip) proteins have been shown to play a regulatory role in vascular differentiation. The hybrid aspen (Populus tremulaxPopulus alba) class III HD-Zip transcription factor (PtaHB1) and microRNA 166 (Pta-miR166) family were cloned from hybrid aspen using a combination of in silico and polymerase chain reaction methods. Expression analyses of PtaHB1 and Pta-miR166 were performed by Northern blot analysis. The expression of PtaHB1 was closely associated with wood formation and regulated both developmentally and seasonally, with the highest expression during the active growing season. Also, its expression was inversely correlated with the level of Pta-miR166. Pta-miR166-directed cleavage of PtaHB1 in vivo was confirmed using modified 5'-rapid amplification of cDNA ends (RACE). The expression of Pta-miR166 was much higher in the winter than in the growing seasons, suggesting seasonal and developmental regulation of microRNA in this perennial plant species.

Amino Acid Sequence↗

PubMed2005

Transcriptome profiling of vertical stem segments provides insights into the genetic regulation of secondary growth in hybrid aspen trees.

In order to better understand the genetic regulation of secondary growth in hybrid aspen (Populus tremula L.xP. alba L.), we carried out a series of cDNA-amplified fragment length polymorphism (AFLP)-based transcriptome analyses in vertical stem segments that represent a gradient of developmental stages with regard to secondary growth. This approach allowed us to screen >80% of the transcriptome expressed in six samples and identify genes differentially expressed with the progress of secondary growth, in a tissue-specific manner. Of the 76,800 transcript-derived fragments (TDFs) analyzed, 271 TDFs were selected and sequenced based on their differential expression patterns. Many of the xylem-up-regulated genes were involved in cell wall and lignin biosynthesis, while the bark-up-regulated genes had diverse functional roles. About 25% of the xylem-up-regulated TDFs analyzed were involved in the phenylpropanoid biosynthesis pathway, which produces the cell wall polymer lignin and various wood extractives. In addition, many of the TDFs showing secondary xylem-specific expression were annotated as genes not previously reported in Populus, including novel cell death proteins, cytoskeleton-interacting proteins, transporters and putative transcription factors.

Blotting, Northern↗

PubMed2004

Plant body weight-induced secondary growth in Arabidopsis and its transcription phenotype revealed by whole-transcriptome profiling.

Wood is an important raw material and environmentally cost-effective renewable source of energy. However, the molecular biology of wood formation (i.e. secondary growth) is surprisingly understudied. A novel experimental system was employed to study the molecular regulation of secondary xylem formation in Arabidopsis. First, we demonstrate that the weight carried by the stem is a primary signal for the induction of cambium differentiation and the plant hormone, auxin, is a downstream carrier of the signal for this process. We used Arabidopsis whole-transcriptome (23 K) GeneChip analysis to examine gene expression profile changes in the inflorescent stems treated for wood formation by cultural manipulation or artificial weight application. Many of the genes up-regulated in wood-forming stems had auxin responsive cis-acting elements in their promoter region, indicating auxin-mediated regulation of secondary growth. We identified 700 genes that were differentially expressed during the transition from primary growth to secondary growth. More than 40% of the genes that were up-regulated (>5x) were associated with signal transduction and transcriptional regulation. Biological significance of these regulatory genes is discussed in light of the induction and development of secondary xylem.

Arabidopsis↗

PubMed2004

Functional characterization of allantoinase genes from Arabidopsis and a nonureide-type legume black locust.

The availability of nitrogen is a limiting factor for plant growth in most soils. Allantoin and its degradation derivatives are a group of soil heterocyclic nitrogen compounds that play an essential role in the assimilation, metabolism, transport, and storage of nitrogen in plants. Allantoinase is a key enzyme for biogenesis and degradation of these ureide compounds. Here, we describe the isolation of two functional allantoinase genes, AtALN (Arabidopsis allantoinase) and RpALN (Robinia pseudoacacia allantoinase), from Arabidopsis and black locust (Robinia pseudoacacia). The proteins encoded by those genes were predicted to have a signal peptide for the secretory pathway, which is consistent with earlier biochemical work that localized allantoinase activity to microbodies and endoplasmic reticulum (Hanks et al., 1981). Their functions were confirmed by genetic complementation of a yeast mutant (dal1) deficient in allantoin hydrolysis. The absence of nitrogen in the medium increased the expression of the genes. In Arabidopsis, the addition of allantoin to the medium as a sole source of nitrogen resulted in the up-regulation of the AtALN gene. The black locust gene (RpALN) was differentially regulated in cotyledons, axis, and hypocotyls during seed germination and seedling growth, but was not expressed in root tissues. In the trunk wood of a mature black locust tree, the RpALN gene was highly expressed in the bark/cambial region, but had no detectable expression in the sapwood or sapwood-heartwood transition zone. In addition, the gene expression in the bark/cambial region was up-regulated in spring and fall when compared with summer, suggesting its involvement in nitrogen mobilization.

Allantoin↗

PubMed2004

Arabidopsis whole-transcriptome profiling defines the features of coordinated regulations that occur during secondary growth.

Secondary growth in the inflorescence stems of Arabidopsis plants was induced by a combination of short-day and long-day treatments. The induced stems were divided into three different stem developmental stages (i.e., immature, intermediate, and mature) with regard to secondary growth. Whole transcriptome microarrays were used to examine the changes in global gene expression occurring at the different stem developmental stages. Over 70% of the Arabidopsis transcriptome was expressed in the stem tissues. In the mature stems with secondary growth, 567 genes were upregulated 5-fold or higher and 530 were downregulated, when compared to immature stems (with no secondary growth) and 10-day old seedlings (with no inflorescence stem). The transcription phenotypes obtained from the stems at different developmental stages largely confirm the existing insights into the biochemical processes involved in the sequential events that lead to wood formation. The major difference found between the stems undergoing secondary growth and only primary growth was in the expression profiles of transcriptional regulation-and signal transduction-related genes. An analysis of several shoot apical meristem (SAM) activity-related gene expression patterns in the stems indicated that the genetic control of secondary meristem activity might be governed by a different mechanism from that of SAM. The current study established the expression patterns of many unknown genes and identified candidate genes that are involved in the genetic regulation of secondary growth. The findings described in this report should improve our understanding of the molecular mechanisms that regulate the growth and development of the stem.

Apoptosis↗

PubMed2004

Seasonal changes in gene expression at the sapwood-heartwood transition zone of black locust (Robinia pseudoacacia) revealed by cDNA microarray analysis.

Heartwood is a determining factor of wood quality and understanding the biology of heartwood may allow us to control its formation. Heartwood formation is a form of senescence that is accompanied by a variety of metabolic alterations in ray parenchyma cells at the sapwood-heartwood transition zone. Although senescence has been studied at the molecular level with respect to primary growth, the cell maturation and death events occurring during heartwood formation have been difficult to study because of their location and timing. Analysis of global gene expression patterns during the transition from sapwood to heartwood may offer a powerful means of identifying the mechanisms controlling heartwood formation. Previously, we developed cDNA microarrays carrying 2567 unigenes derived from the bark/cambium region, sapwood and transition zone of a mature black locust tree. Here, we describe the use of these microarrays to characterize seasonal changes in the expression patterns of 1873 genes from the transition zone of mature black locust trees. When samples collected in summer and fall were compared, 569 genes showed differential expression patterns: 293 genes were up-regulated (> twofold) in summer (July 5) and 276 genes were up-regulated in fall (November 27). More than 50% of the secondary and hormone metabolism-related genes on the microarrays were up-regulated in summer. Twenty-nine out of 55 genes involved in signal transduction were differentially regulated, suggesting that the ray parenchyma cells located in the innermost part of the trunk wood react to seasonal changes. We established the expression patterns of 349 novel genes (previously unknown or no-hit), of which 154 were up-regulated in summer and 195 were up-regulated in the fall.

Gene Expression Regulation, Plant↗

PubMed2003

Transcriptional regulation of secondary growth in Arabidopsis thaliana.

Despite its economic and environmental significance, understanding the molecular biology of secondary growth (i.e. wood formation) in tree species has been lagging behind that of primary growth, primarily due to the inherent difficulties of tree biology. In recent years, Arabidopsis has been shown to express all of the major components of secondary growth. Arabidopsis was induced to undergo secondary growth and the transcriptome profile changes were surveyed during secondary growth using 8.3 K Arabidopsis Genome Arrays. Twenty per cent of the approximately 8300 genes surveyed in this study were differentially regulated in the stems treated for wood formation. Genes of unknown function made up the largest category of the differentially expressed genes, followed by transcription regulation-related genes. Examination of the expression patterns of the genes involved in the sequential events of secondary growth (i.e. cell division, cell expansion, cell wall biosynthesis, lignification, and programmed cell death) identified several key candidate genes for the genetic regulation of secondary growth. In order to gain further insight into the transcriptional regulation of secondary growth, the expression patterns of the genes encoding transcription factors were documented in relation to secondary growth. A computational biology approach was used to identify regulatory cis-elements from the promoter regions of the genes that were up-regulated in wood-forming stems. The expression patterns of many previously unknown genes were established and various existing insights confirmed. The findings described in this report should add new information that can lead to a greater understanding of the secondary xylem formation process.

Arabidopsis↗

PubMed2003

Novel gene expression profiles define the metabolic and physiological processes characteristic of wood and its extractive formation in a hardwood tree species, Robinia pseudoacacia.

Wood is of critical importance to humans as a primary feedstock for biofuel, fiber, solid wood products, and various natural compounds including pharmaceuticals. The trunk wood of most tree species has two distinctly different regions: sapwood and heartwood. In addition to the major constituents, wood contains extraneous chemicals that can be removed by extraction with various solvents. The composition and the content of the extractives vary depending on such factors as, species, growth conditions, and time of year when the tree is cut. Despite the great commercial and keen scientific interest, little is known about the tree-specific biology of the formation of heartwood and its extractives. In order to gain insight on the molecular regulations of heartwood and its extractive formation, we carried out global examination of gene expression profiles across the trunk wood of black locust (Robinia pseudoacacia L.) trees. Of the 2,915 expressed sequenced tags (ESTs) that were generated and analyzed in the current study, 55.3% showed no match to known sequences. Cluster analysis of the ESTs identified a total of 2278 unigene sets, which were used to construct cDNA microarrays. Microarray hybridization analyses were then performed to survey the changes in gene expression profiles of trunk wood. The gene expression profiles of wood formation differ according to the region of trunk wood sampled, with highly expressed genes defining the metabolic and physiological processes characteristic of each region. For example, the gene encoding sugar transport had the highest expression in the sapwood, while the structural genes for flavonoid biosynthesis were up-regulated in the sapwood-heartwood transition zone. This analysis also established the expression patterns of 341 previously unknown genes.

DNA, Complementary↗

PubMed2003

Transcriptome analysis reveals novel features of the molecular events occurring in the laticifers of Hevea brasiliensis (para rubber tree).

Latex of Hevea brasiliensis (Willd. ex A, Juss.) Mull. Arg. (Brazilian rubber tree) contains 30-50% (w/w) of natural rubber (cis-1,4-polyisoprene), which is an important raw material for many industrial uses. In order to gain insights into the molecular events occurring in latex, we analyzed more than 20,000 cDNA-AFLP-based TDFs (transcription-derived fragments) and 1176 ESTs. The results revealed several novel features of the latex transcriptome. First, the repertoire of the genes expressed in latex is unique. Only seven gene families accounted for more than 51% of the latex transcriptome. Among them, two of the most abundant ESTs were the genes encoding rubber particle proteins REF (rubber elongation factor) and SRPP (small rubber particle protein), comprising 29% of the total ESTs. Unexpectedly, several genes involved in the rubber biosynthesis were expressed at low levels in the latex. In fact, genes encoding cis -prenyltransferase (CPT), a potential candidate for rubber polymerase, were not present in the EST pool because of their low expression level. However, we were able to clone four full-length cDNAs by screening the same latex cDNA library used in the EST analysis and confirmed their enzyme activity in vitro. The second most abundant transcripts were defense- or stress-related genes, suggesting that defense is one of the functions of laticifers. Finally, the presence of the non-mevalonate DXP/MEP pathway for IPP synthesis in latex was noted by up-regulation of the 1-deoxy-D-xylulose 5-phosphate synthase gene.

Amino Acid Sequence↗

PubMed2003

An auxin-repressed gene (RpARP) from black locust (Robinia pseudoacacia) is posttranscriptionally regulated and negatively associated with shoot elongation.

The plant hormone auxin regulates various growth and developmental processes by controlling the expression of auxin-response genes. While many genes up-regulated by auxin have been characterized, less is known about the genes that are down-regulated by auxin. We isolated and characterized an auxin-repressed gene (RpARP) from the tree legume, Robinia pseudoacacia L. A sequence similarity search in public databases showed that the RpARP gene has homologs in various higher plants including monocots and dicots. The deduced amino acid sequences are highly conserved among these homologs (up to 85% identity). Northern blot analysis showed that auxin repressed RpARP gene expression and that repression was dependent on the presence of metabolizable sugar and on protein synthesis. In addition, cold treatment abolished the auxin-mediated repression of RpARP gene expression. Results from transgenic plant analyses suggest that RpARP gene expression is posttranscriptionally regulated by auxin and by the untranslated regions. Sequence analysis of the promoter region (-70 and -500 bp upstream of the putative transcription initiation site) of the RpARP gene identified four sucrose-repressible response elements (TATCCAT-motifs; Huang et al. 1990), suggesting that the cis-elements responsible for regulation by sucrose are located in the promoter region. In fact, the expression of the transgenic RpARP gene was unaffected by sucrose when driven by a CaMV 35S promoter. We present evidence that RpARP gene expression is negatively associated with hypocotyl elongation.

Arabidopsis↗

PubMed2000

Genes expressed in the latex of Hevea brasiliensis.

Rubber (cis-1,4-polyisoprene), an important raw material for many industrial uses, is synthesized in the latex of Hevea brasiliensis (Willd. ex A. Juss.) Müll. Arg. We postulated that the genes uniquely or preferentially expressed in the latex may be important for rubber biosynthesis. We constructed cDNA libraries from the latex of H. brasiliensis to investigate the genes expressed in the latex by single-run partial sequencing of the cDNA clones. Sequence analyses identified 245 expressed sequence tags (ESTs), of which 57% showed homology to previously described sequences in public databases. About 16% of the database-matched ESTs encode rubber biosynthesis-related proteins such as rubber elongation factor (REF) and small rubber particle protein (SRPP). The second most frequent transcripts next to rubber biosynthesis-related genes were defense genes and protein metabolism-related genes (12.6% each). About 27% of the database-matched ESTs had sequence homology with genes of unknown function. Among the redundantly expressed genes, REF was the most frequently expressed (6.1%), followed by SRPP (3.7%) and HbLAR (2.9%). Northern blot analyses showed that ten (71%) of the 14 ESTs studied were expressed at a higher level in latex than in leaves.

Journal Article↗