• Molecules and Cells
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• v.26 no.3
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• pp.236-242
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• 2008

Invertase (${\beta}$-D-fructofuranosidase; EC 3.2.1.26) catalyzes the conversion of sucrose into glucose and fructose and is involved in an array of important processes, including phloem unloading, carbon partitioning, the response to pathogens, and the control of cell differentiation and development. Its importance may have caused the invertases to evolve into a multigene family whose members are regulated by a variety of different mechanisms, such as pH, sucrose levels, and inhibitor proteins. Although putative invertase inhibitors in the Arabidopsis genome are easy to locate, few studies have been conducted to elucidate their individual functions in vivo in plant growth and development because of their high redundancy. In this study we assessed the functional role of the putative invertase inhibitors in Arabidopsis by generating transgenic plants harboring a putative invertase inhibitor gene under the control of the CaMV35S promoter. A transgenic plant that expressed high levels of the putative invertase inhibitor transcript when grown under normal conditions was chosen for the current study. To our surprise, the stability of the invertase inhibitor transcripts was shown to be down-regulated by the phytohormone ABA (abscisic acid). It is well established that ABA enhances invertase activity in vivo but the underlying mechanisms are still poorly understood. Our results thus suggest that one way ABA regulates invertase activity is by down-regulating its inhibitor.

• Horticultural Science & Technology
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• v.29 no.2
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• pp.135-143
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• 2011

In the Doritaenopsis hybrid, like most of the orchid species and hybrids, temperature is crucial for the vegetative-to-reproductive transition, and low temperature is required for bud differentiation. To understand the molecular mechanism of this process, an orchid GIGANTEA (GI) gene, DhGI1, was isolated and characterized by using the rapid amplification of cDNA ends (RACE) PCR technique. Sequence analysis showed that the full-length cDNA is 4,022 bp with a major open reading frame of 3,483 bp, and the amino acid sequence showed high similarity to GI proteins in Zea mays, Oryza sativa, Arabidopsis thaliana and other plants. Semi-quantitative RT-PCR revealed that DhGI1 was expressed throughout development and could be detected in roots, stems, leaves, peduncles and flower buds. The expression level of DhGI1 was higher when the plants were flowering at low temperature (22/$18^{\circ}C$ day/night) than the other growth stages. Further analysis indicated that the accumulation of DhGI1 transcripts was significantly increased at low temperature, and concomitantly, initiation of the peduncle was observed. However, DhGI1 levels were low under high temperature (30/$25^{\circ}C$) conditions, and flower initiation was inhibited. These results indicate that the expression of DhGI1 is regulated by low temperature and that DhGI1 may play an important role in inflorescence initiation in this Doritaenopsis hybrid at low temperatures.

• Journal of Life Science
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• v.16 no.4
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• pp.704-709
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• 2006

The present study intends to characterize the DNA damage-inducible responses in Caenorhabditis elegans. To study UV-inducible responses in C. elegans, two UV-inducible cDNA clones were isolated from C. elegans by using subtration hybridization method. To investigate the expression of isolated genes, UV100 and UV150, the cellular levels of the transcript were determined by Northern blot analysis after UV-irradiation. The transcripts of isolated gene increased rapidly and reached maximum accumulation after UV-irradiation. Compared to the message levels of control, the levels of maximal increase were approximately 2 folds to UV-irradiation. These results implied that the effects of damaging agents are complex and different regulatory pathways exist for the induction of these genes. To study the function of UV100 and UV150 gene in response to UV irradiation, we carried out a RNAi experiment and investigated the UV sensivity. This result indicated that UV100 gene involved in stage-specific repair pathway or regulated by development.

• Journal of Radiation Industry
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• v.4 no.4
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• pp.325-334
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• 2010

Transcriptional regulation in response to salt in mutant lines was investigated using oligonucleotide microarrays. In order to characterize the salt-responsive genes in rice, the expression profiles of transcripts that responded to salt-treatment were monitored using the microarrays. In the microarray analysis, among 37,299 reliable genes, 5,101, 2,758 and 2,277 genes were up-regulated by more than 2-fold using the salt treatment, while the numbers of down-regulated genes were 4,619, 3,234, and 1,878 in the WT, ST-495, and ST-532, respectively. From genotype changes induced by gamma ray mutagenesis, 3,345 and 2,397 genes were up-regulated, while 2,745 and 2,075 genes were down-regulated more than 2-fold in the two untreated mutants lines compared with untreated WT, respectively. A total of 3,108 and 2,731 genes were up-regulated more than 2-fold, while 3,987 and 3,660 genes were down-regulated by more than 2-fold in the salt treatment of the two mutants lines compared with the salt treated WT, respectively. The expressions of membrane transporter genes such as OsAKT1, OsKUP, and OsNAC increased more severely in ST-495 and ST-532 than in the WT. The expressions of the proline accumulation related genes such as OsP5CS and OsP5CR were also markedly increased in the salt tolerant mutants when compared to the WT plant.

• Korean Journal of Breeding Science
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• v.42 no.5
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• pp.481-487
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• 2010

The ripening behavior of three apple cultivars, 'Tsugaru', 'Hongro' and 'Fuji' was distinctive and the involvement of POLYGALACTURONASE(PG) in the fruit softening process was confirmed to be ethylene dependent. Fruit softening is genetically coordinated by the action of several cell wall enzymes, including PG which depolymerizes cell wall pectin. Also, loss of firmness is associated with increasing of the ripening hormone, ethylene. In this work, climacteric ripening of three apple cultivars, Tsugaru, Hongro and Fuji, producing different ethylene levels and ripening responses, was examined. Correspondingly in Fuji, a linear and basal ethylene level was observed over the entire period of measurements, and Tsugaru and Hongro displayed a typical climacteric rise in ethylene production. Transcript accumulation of genes involved in ethylene biosynthesis (MdACS3 and MdACO1) and MdPG1 was studied in Tsugaru, Hongro and Fuji cultivars. Expression of MdACO1 transcripts was shown in all three ripened apple fruits. However, the MdACS3 and MdPG1 were transcribed differently in these cultivars. Comparing the MdPG1 of 'Tsugaru', 'Hongro' and 'Fuji', structural difference was discovered by genomic Southern analysis. Overall results pointed out that MdACS3 and MdPG1 play an important role in regulation of fruit ripening in apple cultivar.

• Journal of Microbiology and Biotechnology
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• v.31 no.1
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• pp.79-91
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• 2021

γ-Glutamylcysteine synthetase (Gcs1) and glutathione reductase (Glr1) activity maintains minimal levels of cellular methylglyoxal in Candida albicans. In glutathione-depleted Δgcs1, we previously saw that NAD(H)-linked methylglyoxal oxidoreductase (Mgd1) and alcohol dehydrogenase (Adh1) are the most active methylglyoxal scavengers. With methylglyoxal accumulation, disruptants lacking MGD1 or ADH1 exhibit a poor redox state. However, there is little convincing evidence for a reciprocal relationship between methylglyoxal scavenger genes-disrupted mutants and changes in glutathione-(in)dependent redox regulation. Herein, we attempt to demonstrate a functional role for methylglyoxal scavengers, modeled on a triple disruptant (Δmgd1/Δadh1/Δgcs1), to link between antioxidative enzyme activities and their metabolites in glutathione-depleted conditions. Despite seeing elevated methylglyoxal in all of the disruptants, the result saw a decrease in pyruvate content in Δmgd1/Δadh1/Δgcs1 which was not observed in double gene-disrupted strains such as Δmgd1/Δgcs1 and Δadh1/Δgcs1. Interestingly, Δmgd1/Δadh1/Δgcs1 exhibited a significantly decrease in H2O2 and superoxide which was also unobserved in Δmgd1/Δgcs1 and Δadh1/Δgcs1. The activities of the antioxidative enzymes erythroascorbate peroxidase and cytochrome c peroxidase were noticeably higher in Δmgd1/Δadh1/Δgcs1 than in the other disruptants. Meanwhile, Glr1 activity severely diminished in Δmgd1/Δadh1/Δgcs1. Monitoring complementary gene transcripts between double gene-disrupted Δmgd1/Δgcs1 and Δadh1/Δgcs1 supported the concept of an unbalanced redox state independent of the Glr1 activity for Δmgd1/Δadh1/Δgcs1. Our data demonstrate the reciprocal use of Eapx1 and Ccp1 in the absence of both methylglyoxal scavengers; that being pivotal for viability in non-filamentous budding yeast.

• Molecules and Cells
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• v.45 no.9
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• pp.660-672
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• 2022

The target of rapamycin complex (TORC) plays a key role in plant cell growth and survival by regulating the gene expression and metabolism according to environmental information. TORC activates transcription, mRNA translation, and anabolic processes under favorable conditions, thereby promoting plant growth and development. Tomato fruit ripening is a complex developmental process promoted by ethylene and specific transcription factors. TORC is known to modulate leaf senescence in tomato. In this study, we investigated the function of TORC in tomato fruit ripening using virus-induced gene silencing (VIGS) of the TORC genes, TOR, lethal with SEC13 protein 8 (LST8), and regulatory-associated protein of TOR (RAPTOR). Quantitative reverse transcription-polymerase chain reaction showed that the expression levels of tomato TORC genes were the highest in the orange stage during fruit development in Micro-Tom tomato. VIGS of these TORC genes using stage 2 tomato accelerated fruit ripening with premature orange/red coloring and decreased fruit growth, when control tobacco rattle virus 2 (TRV2)-myc fruits reached the mature green stage. TORC-deficient fruits showed early accumulation of carotenoid lycopene and reduced cellulose deposition in pericarp cell walls. The early ripening fruits had higher levels of transcripts related to fruit ripening transcription factors, ethylene biosynthesis, carotenoid synthesis, and cell wall modification. Finally, the early ripening phenotype in Micro-Tom tomato was reproduced in the commercial cultivar Moneymaker tomato by VIGS of the TORC genes. Collectively, these results demonstrate that TORC plays an important role in tomato fruit ripening by modulating the transcription of various ripening-related genes.

• Journal of Plant Biotechnology
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• v.45 no.2
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• pp.90-101
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• 2018

Strawberry (Fragaria ${\times}$ ananassa) is a globally-cultivated and popular fruit crop, prized for its flavor and nutritional value. Sweetness, a key determinant of fruit quality, depends on the sugar composition and concentration. We selected eight strawberry cultivars based on the fruit soluble solids content to represent high and low sugar content groups. The average soluble solid content was $13.6^{\circ}Brix$ (Okmae, Geumsil, Aram, and Maehyang) and $2.9^{\circ}Brix$ (Missionary, Camino Real, Portola, and Gilgyung53), for the high and low sugar content groups, respectively. Sucrose was the main sugar in the cultivars with high sugar content, whereas fructose was the main component in the low sugar content cultivars. Fruit starch concentration ranged from $3.247{\pm}0.056$ to $3.850{\pm}0.055g/100g$, with a 12% higher concentration in the high sugar content cultivars. Additionally, we identified 41 sugar metabolism-related genes in Fragaria ${\times}$ ananassa and analyzed the relationship between their transcripts and the sugar accumulation in fruit. FaGPT1, FaTMT1, FaHXK1, FaPHS1, FaINVA-3, and FacxINV2-1 were highly expressed in the high sugar content cultivars, while FapGlcT, FaTMT2-1, FaPHS2-1, FaSUSY1-1, and FaSUSY1-2 were highly expressed in the low sugar content cultivars. In general, a greater number of genes encoding sugar transporters or involved in sugar synthesis were highly expressed in the high sugar content cultivars. Contrarily, genes involved in sugar degradation were preferentially transcribed in the low sugar content cultivars. Although gene expression was not perfectly proportional to sugar content or concentration, our analysis of the genes involved in sugar metabolism and accumulation in strawberries provides a framework for further studies and for the subsequent engineering of sugar metabolism to enhance fruit quality.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.6
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• pp.880-884
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• 2001

Rumen microbiology research has undergone several evolutionary steps: the isolation and nutritional characterization of readily cultivated microbes; followed by the cloning and sequence analysis of individual genes relevant to key digestive processes; through to the use of small subunit ribosomal RNA (SSU rRNA) sequences for a cultivation-independent examination of microbial diversity. Our knowledge of rumen microbiology has expanded as a result, but the translation of this information into productive alterations of ruminal function has been rather limited. For instance, the cloning and characterization of cellulase genes in Escherichia coli has yielded some valuable information about this complex enzyme system in ruminal bacteria. SSU rRNA analyses have also confirmed that a considerable amount of the microbial diversity in the rumen is not represented in existing culture collections. However, we still have little idea of whether the key, and potentially rate-limiting, gene products and (or) microbial interactions have been identified. Technologies allowing high throughput nucleotide and protein sequence analysis have led to the emergence of two new fields of investigation, genomics and proteomics. Both disciplines can be further subdivided into functional and comparative lines of investigation. The massive accumulation of microbial DNA and protein sequence data, including complete genome sequences, is revolutionizing the way we examine microbial physiology and diversity. We describe here some examples of our use of genomics- and proteomics-based methods, to analyze the cellulase system of Ruminococcus flavefaciens FD-1 and explore the genome of Ruminococcus albus 8. At Illinois, we are using bacterial artificial chromosome (BAC) vectors to create libraries containing large (>75 kbases), contiguous segments of DNA from R. flavefaciens FD-1. Considering that every bacterium is not a candidate for whole genome sequencing, BAC libraries offer an attractive, alternative method to perform physical and functional analyses of a bacterium's genome. Our first plan is to use these BAC clones to determine whether or not cellulases and accessory genes in R. flavefaciens exist in clusters of orthologous genes (COGs). Proteomics is also being used to complement the BAC library/DNA sequencing approach. Proteins differentially expressed in response to carbon source are being identified by 2-D SDS-PAGE, followed by in-gel-digests and peptide mass mapping by MALDI-TOF Mass Spectrometry, as well as peptide sequencing by Edman degradation. At Ohio State, we have used a combination of functional proteomics, mutational analysis and differential display RT-PCR to obtain evidence suggesting that in addition to a cellulosome-like mechanism, R. albus 8 possesses other mechanisms for adhesion to plant surfaces. Genome walking on either side of these differentially expressed transcripts has also resulted in two interesting observations: i) a relatively large number of genes with no matches in the current databases and; ii) the identification of genes with a high level of sequence identity to those identified, until now, in the archaebacteria. Genomics and proteomics will also accelerate our understanding of microbial interactions, and allow a greater degree of in situ analyses in the future. The challenge is to utilize genomics and proteomics to improve our fundamental understanding of microbial physiology, diversity and ecology, and overcome constraints to ruminal function.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.20-20
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• 2017

Plant genomes include heterochromatic loci that consist of repetitive sequences and transposable elements. LTR retrotransposon is the major class of transposons in advanced plants in terms of proportion in plant genome. The elements contribute not only to genome size but also to genome stability and gene expression. A number of cases have been reported transposon insertions near genic regions affect crop traits such as fruit pigments, stress tolerance, and yields. Functional LTR retrotransposons produce extrachromosomal DNA from genomic RNA by reverse transcription that takes place within virus-like-particles (VLPs). DECREASED DNA METHYLATION 1 (DDM1) plays important roles in maintaining DNA methylation of heterochromatin affecting all sequence contexts, CG, CHG, and CHH. Previous studies showed that ddm1 mutant exhibits massive transcription of retrotransposons in Arabidopsis, but only few of them were able to create new insertions into the genome. RNA-dependent RNA POLYMERASE 6 (RDR6) is known to function in restricting accumulation of transposon RNA by processing the transcripts into 21-22 nt epigenetically activated small interfering RNA (easiRNA). We purified VLPs and sequence cDNA to identify functional LTR retrotransposons in Arabidopsis ddm1 and ddm1rdr6 plants. Over 20 LTR copia and gypsy families were detected in ddm1 and ddm1rdr6 sequencing libraries and most of them were not reported for mobility. In ddm1rdr6, short fragments of ATHILA gypsy elements were detected. It suggests easiRNAs might regulate reverse transcription steps. The highest enriched element among transposon loci was previously characterized EVADE element. It has been reported that active EVADE element is more efficiently silenced through female germline than male germline. By genetic analyses, we found ddm1 and rdr6 mutation affect maternal silencing of active EVADE elements. DDM1-GFP protein accumulated in megaspore mother cell but was not found in mature egg cell. The fusion protein was also found in early embryo and maternal DDM1-GFP allele was more dominantly expressed in the embryo. We observed localization of DDM1-GFP in Arabidopsis and DDM1-YFP in maize and found the proteins accumulated in dividing zone of root tips. Currently we are looking at cell cycle dependency of DDM1 expression using maize system. Among 10 AGO proteins in Arabidopsis, AGO9 is specifically expressed in egg cell and shoot meristematic cells. In addition, mutation of AGO9 and RDR6 caused failure in maternal silencing, implying 21-22 nt easiRNA pathway is important for retrotransposon silencing in female gametophyte or/and early embryo. On the other hand, canonical 24 nt sRNA-directed DNA methylation (RdDM) pathways did not contribute to maternal silencing as confirmed by this study. Heat-activated LTR retrotransposon, ONSEN, was not silenced by DDM1 but the silencing mechanisms require RdDM pathways in somatic cells. We will propose distinct mechanisms of LTR retrotransposons in germline and somatic stages.