Tuan-Hua David Ho

Academia Sinica

Background Cultivation of rice (Oryza sativa) started in Taiwan about 5000 years ago. Here we studied changes in the rice population during this period by using archaeological, morphological, genetic and genomic strategies. We studied the grain size changes of carbonized rice from excavated sites. We also revealed the variations in landraces collec...

Water deficit stress causes devastating loss of crop yield worldwide. Improving crop drought resistance has become an urgent issue. Here we report that a group of abscisic acid (ABA)/drought stress-induced monocot-specific, intrinsically disordered, and highly proline-rich proteins, REPETITIVE PROLINE-RICH PROTEINS (RePRPs), play pivotal roles in d...

The aim of this study was to develop an efficient bioinoculant for amelioration of adverse effects from chilling stress (10°C), which are frequently occurred during rice seedling stage. Seed germination bioassay under chilling condition with rice (Oryza sativa L.) cv. Tainan 11 was performed to screen for plant growth-promoting (PGP) bacteria among...

Background β-1,4-endoglucanase (EG) is one of the three types of cellulases used in cellulose saccharification during lignocellulosic biofuel/biomaterial production. GsCelA is an EG secreted by the thermophilic bacterium Geobacillus sp. 70PC53 isolated from rice straw compost in southern Taiwan. This enzyme belongs to glycoside hydrolase family 5 (...

Background β-Glucosidases are essential for cellulose hydrolysis by catalyzing the final cellulolytic degradation of cello-oligomers and cellobiose to glucose. D2-BGL is a fungal glycoside hydrolase family 3 (GH3) β-glucosidase isolated from Chaetomella raphigera with high substrate affinity, and is an efficient β-glucosidase supplement to Trichode...

Background Lignocellulolytic enzymes are essential for agricultural waste disposal and production of renewable bioenergy. Many commercialized cellulase mixtures have been developed, mostly from saprophytic or endophytic fungal species. The cost of complete cellulose digestion is considerable because a wide range of cellulolytic enzymes is needed. H...

Intrinsically disordered proteins function as flexible stress modulators in vivo through largely unknown mechanisms. Here, we elucidated the mechanistic role of an intrinsically disordered protein, REPETITIVE PROLINE-RICH PROTEIN (RePRP), in regulating rice (Oryza sativa) root growth under water deficit. With nearly 40% proline, RePRP is induced by...

Grain/seed yield and plant stress tolerance are two major traits that determine the yield potential of many crops. In cereals, grain size is one of the key factors affecting grain yield. Here, we identify and characterize a newly‐discovered gene Rice Big Grain 1 (RBG1) that regulates grain and organ development, as well as abiotic stress tolerance....

Most crops cannot germinate underwater. Rice exhibits certain degrees of tolerance to oxygen (O2) deficiency for anaerobic germination (AG) and anaerobic seedling development (ASD). Direct rice seeding, whereby seeds are sown into soil rather than transplanting seedlings from the nursery, becomes an increasingly popular cultivation method due to la...

Background: To produce second-generation biofuels, enzymatic catalysis is required to convert cellulose from lignocellulosic biomass into fermentable sugars. β-Glucosidases finalize the process by hydrolyzing cellobiose into glucose, so the efficiency of cellulose hydrolysis largely depends on the quantity and quality of these enzymes used during...

Significance As autotrophic organisms, sugar status in plants must be constantly monitored and reacted to in order to maintain sugar homeostatic states crucial for growth regulation, environmental stress tolerance, and productivity. α-Amylase (αAmy) is the key enzyme hydrolyzing starch into sugars and is regulated by sugar levels; it is induced by...

Laccases that are tolerant to organic solvents are powerful bio-catalysts with broad applications in biotechnology. Most of these uses must be accomplished at high concentration of organic solvents, during which proteins undergo unfolding, thereby losing enzyme activity. Here we show that organic-solvent pre-incubation provides effective and revers...

Ectopic expression of the rice WINDING 1 (WIN1) gene leads to a spiral phenotype only in shoots but not in roots. Rice WIN1 belongs to a specific class of proteins in cereal plants containing a Bric-a-Brac/Tramtrack/Broad (BTB) complex, a non-phototropic hypocotyl 3 (NPH3) domain and a coiled-coil motif. The WIN1 protein is predominantly localized...

Background: Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environment-friendly way becomes increasingly important. Therefore, rice research community needs to share resources to better understand functions of rice genes that are the foundation for f...

Seeds serve as a great model to study plant responses to drought stress, which is largely mediated by abscisic acid (ABA). The ABA responsive element (ABRE) is a key cis-regulatory element in ABA signaling. However, its consensus sequence, (ACGTG(G/T)C), is present in the promoters of only about 40% of ABA induced genes in rice aleurone cells, sugg...

A major challenge of modern agricultural biotechnology is the optimization of plant architecture for enhanced productivity, stress tolerance and water use efficiency (WUE). To optimize plant height and tillering that directly link to grain yield in cereals and are known to be tightly regulated by gibberellins (GAs), we attenuated the endogenous lev...

Cellulases from Bacillus and Geobacillus bacteria are potentially useful in the biofuel and animal feed industries. One of the unique characteristics of these enzymes is that they are usually quite thermostable. We previously identified a cellulase, GsCelA, from thermophilic Geobacillus sp. 70PC53, which is much more thermostable than its Bacillus...

Communication between source organs (exporters of photoassimilates) and sink organs (importers of fixed carbon) has a pivotal role in carbohydrate assimilation and partitioning during plant growth and development. Plant productivity is enhanced by sink strength and source activity, which are regulated by a complex signaling network encompassing sug...

Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in u...

In a transgenic plant, a stress-responsive promoter containing CE3 and ABRE2 from HVA1 ABRC3 and CE1 from HVA22 ABRC1, directs low background expression of a gene under normal growth conditions, but is highly inducible by an abiotic stress, such as abscisic acid, dehydration, salt or cold. Compared with the wild type plant, the transgenic plant tha...

Regulation of root architecture is essential for maintaining plant growth under adverse environment. A synthetic abscisic acid (ABA)/stress-inducible promoter was designed to control the expression of a late embryogenesis abundant protein (HVA1) in transgenic rice. The background of HVA1 is low but highly inducible by ABA, salt, dehydration and col...

Drought is one of the major abiotic stresses that affect productivity in soybean (Glycine max L.) Several genes induced by drought stress include functional genes and regulatory transcription factors. The Arabidopsis thaliana DREB1D transcription factor driven by the constitutive and ABA-inducible promoters was introduced into soybean through Agrob...

Cellulosic biomass is an abundant and promising energy source. To make cellulosic biofuels competitive against conventional fuels, conversion of rigid plant materials into sugars must become efficient and cost-effective. During cellulose degradation, cellulolytic enzymes generate cellobiose (β-(1→4)-glucose dimer) molecules, which in turn inhibit s...

A method of making a transgenic plant by transforming into a host plant a recombinant DNA construct that expresses in the transgenic plant a rice polypeptide and the transgenic plant thus produced.

In plants, source-sink communication plays a pivotal role in crop productivity, yet the underlying regulatory mechanisms are largely unknown. The SnRK1A protein kinase and transcription factor MYBS1 regulate the sugar starvation signaling pathway during seedling growth in cereals. Here, we identified plant-specific SnRK1A-interacting negative regul...

IIn the root of rice (Oryza sativa L.), ABA treatment, salinity or water-deficit stress induces the expression of a family of four genes, Repetitive Proline Rich Protein (RePRP). These genes encode two subclasses of novel proline-rich glycoproteins with highly repetitive PX1PX2 motifs, RePRP1 and RePRP2. RePRP orthologues exist only in monocotyledo...

Novel gibberellin 2-oxidase (GA2ox) genes were identified. Differential expression of GA2ox genes correlated with flower development, seed germination, tiller growth and other developmental processes. In addition, the early and increased growth of tiller and adventitious root and altered root architecture caused by overexpression of GA2oxs further...

A novel beta-glucosidase and nucleic acids encoding the beta-glucosidase. Also disclosed are cells, compositions, and methods relating to using the beta-glucosidase to convert ligocellulosic material to fermentable sugars.

Over the years, culturable cellulase-producing microorganisms have been isolated from a variety of sources and genes of cellulolytic enzymes have been cloned. Then again, the "great plate count anomaly" phenomenon necessitates a culture-independent metagenomic approach for the isolation of cellulolytic genes from microorganisms in their natural env...

Germination is a unique developmental transition from metabolically quiescent seed to actively growing seedling that requires an ensemble of hydrolases for coordinated nutrient mobilization to support heterotrophic growth until autotrophic photosynthesis is established. This study reveals two crucial transcription factors, MYBS1 and MYBGA, present...

Wood feeding insects depends heavily on the secretion of a combination of cellulases, mainly endoglucanases and other glucanases such as exoglucanases and xylanases, for efficient digestion of the cellulosic materials. To date, although a high number of endoglucanases have been found in xytophagous insects, little is known about exoglucanases encod...

Drought, extreme temperatures and high salinity are major limiting factors for plant growth and crop productivity. In their quest to feed the ever-increasing world population, agricultural scientists have to contend with these adverse environmental factors. If crops can be redesigned to better cope with abiotic stress, agricultural production can b...

Bacillus subtilis is most commonly employed for secretion of recombinant proteins. To circumvent the problems caused by using plasmids, the T7 expression system known for its high efficiency was rebuilt in B. subtilis. Accordingly, a markerless and replicon-free method was developed for genomic insertion of DNAs. By the act of homologous recombinat...

A high yield of beta-glucosidase (EC 3.2.1.21) of 159.1 U/g-solid activity on 4-nitrophenyl beta-d-glucopyranoside (pNPG) was achieved by rice bran-based solid-state fermentation (SSF) of the recently characterized fungus Penicillium citrinum YS40-5. The enzyme was both thermophilic and acidophilic at the optimized temperature and pH of 70 degrees...

Flooding is a widespread natural disaster that leads to oxygen (O(2)) and energy deficiency in terrestrial plants, thereby reducing their productivity. Rice is unusually tolerant to flooding, but the underlying mechanism for this tolerance has remained elusive. Here, we show that protein kinase CIPK15 [calcineurin B-like (CBL)-interacting protein k...

A thermophilic Geobacillus bacterium secreting high activity of endo-glucanase (EC 3.2.1.4) was isolated from rice straw compost supplemented with pig manure. A full-length gene of 1,104 bp, celA, encoding this glycosyl hydrolase family 5 endo-glucanase of 368 amino acids was isolated. No related gene from Geobacillus has been reported previously....

Abscisic acid (ABA) and gibberellins (GAs) control several developmental processes including seed maturation, dormancy, and germination. The antagonism of these two hormones is well-documented. However, recent data from transcription profiling studies indicate that they can function as agonists in regulating the expression of many genes although th...

Autophagy is an intracellular process in which a portion of cytoplasm is transported into vacuoles for recycling. Physiological roles of autophagy in plants include recycling nutrients during senescence, sustaining life during starvation, and the formation of central digestive vacuoles. The regulation of autophagy and the formation of autophagosome...

Plant HVA22 is a unique abscisic acid (ABA)/stress-induced protein first isolated from barley (Hordeum vulgare) aleurone cells. Its yeast homolog, Yop1p, functions in vesicular trafficking and in the endoplasmic reticulum (ER) network in vivo. To examine the roles of plant HVA22, barley HVA22 was ectopically expressed in barley aleurone cells. Over...

Promoters play key roles in conferring temporal, spatial, chemical, developmental, or environmental regulation of gene expression. Promoters that are subject to specific regulations are useful for manipulating foreign gene expression in plant cells, tissues, or organs with desirable patterns and under controlled conditions, and have been important...

We describe an efficient inducible system to regulate gene expression in plants based on quorum-sensing components found in Gram-negative bacteria such as Agrobacterium tumefaciens. These bacteria monitor their own population density by utilizing members of the N-acyl homoserine lactone family as inducers and a transcriptional activator as its rece...

A monoclonal antibody prepared against barley (Hordeum vulgare L., cv. Himalaya) nuclease (EC 3.1.30.2) was characterized with solid-state enzyme-linked immunosorbent assays and immuno-blotting. The antibody was specific for intracellular and secreted nuclease. Hormonal regulation of the synthesis and secretion of nuclease in isolated aleurone laye...

The intracellular localization of an endonuclease (nuclease I) in barley aleurone responding to gibberellic acid was investigated by subcellular fractionation and immunocytochemistry with monoclonal and polyclonal antibodies. Organelle separations were performed with aleurone layers and protoplasts; immunefixations were carried out on protoplasts o...

Motivation: A fundamental problem of computational genomics is identifying the genes that respond to certain endogenous cues and environmental stimuli. This problem can be referred to as targeted gene finding. Since gene regulation is mainly determined by the binding of transcription factors and cis-regulatory DNA sequences, most existing gene ann...

A new member of the cereal PKABA1 subfamily of protein kinases, TtPK1, was isolated from Triticum tauschii, a diploid progenitor of hexaploid wheat, Triticum aestivum. The full-length TtPK1 cDNA was cloned from a library derived from vegetative tissues from 26 d old light grown T. tauschii seedlings. TtPK1 cDNA hybridizes to transcripts that are up...

The barley bZIP transcription factor HvABI5 mediates abscisic acid (ABA)-upregulated gene expression in barley (Hordeum vulgare L.) seeds. HvABI5 specifically recognizes cis-elements of the ABA response complexes present in the promoters of the ABA-induced genes HVA1 and HVA22. HvABI5 together with another transcription factor, HvVP1, are required...

Duplicate loci offer a very powerful system for understanding the complicated genome structure and adaptive evolution of a gene family. In this study, the genetic variation at paralogs AtHVA22d and AtHVA22e, members of an ABA- and stress-inducible gene family, is examined in the selfing Arabidopsis thaliana. Population genetic analysis indicates co...

The molecular mechanism by which GA regulates plant growth and development has been a subject of active research. Analyses of the rice (Oryza sativa) genomic sequences identified 77 WRKY genes, among which OsWRKY71 is highly expressed in aleurone cells. Transient expression of OsWRKY71 by particle bombardment specifically represses GA-induced Amy32...

Drought is by far the leading environmental stress-limiting crop yields world-wide. Genetic engineering techniques hold great promise for developing crop cultivars with drought tolerance. Transgenic rice plants have been developed by engineering a wide variety of genes and were shown to be drought tolerant. Understanding the mechanism of stress tol...

Abscisic acid (ABA)-response promoter complexes (ABRCs), consisting of an ACGT core-containing element (ACGT box) and a coupling element (CE), have been shown to be necessary and sufficient for ABA induction of gene expression in cereal plants. In this work, the component elements of two ABRCs are defined in terms of base sequence, orientation, and...

Modern-day plants are subjected to various biotic and abiotic stresses thereby limiting plant productivity and quality. It has previously been reported that the use of a strong constitutive 35S cauliflower mosaic virus (CaMV) promoter to drive the expression of Arabidopsis CBF1 in tomato improved tolerance to cold, drought and salt loading, at the...

The abscisic acid (ABA) response promoter complexes (ABRCs) of the HVA1 and HVA22 genes have been shown to confer ABA-induced gene expression in cereals. A barley basic domain/Leu zipper (bZIP) transcription factor, HvABI5, is able to recognize ABRCs in vitro in a sequence-specific manner and to transactivate ABRC-beta-glucuronidase reporter genes...

The antagonism between gibberellins (GA) and abscisic acid (ABA) is an important factor regulating the developmental transition from embryogenesis to seed germination. In cereal aleurone layers, the expression of genes encoding hydrolytic enzymes needed for seedling growth, such as -amylases and proteases, is induced by GA but suppressed by ABA. In...

Expression of the barley (Hordeum vulgare) HVA22 gene is induced by environmental stresses, such as dehydration, salinity, and extreme temperatures, and by a plant stress hormone, abscisic acid. Genes sharing high level of sequence similarities with HVA22 exist in diverse eukaryotic organisms, including animals, plants, and fungi, but not in any pr...

The interaction between two phytohormones, gibberellins (GA) and abscisic acid (ABA), is an important factor regulating the developmental transition from seed dormancy to germination. In cereal aleurone tissue, GA induces and ABA suppresses the expression of alpha-amylases that are essential for the utilization of starch stored in the endosperm. In...