• Korean Journal of Environmental Agriculture
• /
• v.32 no.1
• /
• pp.48-54
• /
• 2013

BACKGROUND: Sorghum (Sorghum bicolor (L.) Moench) ranks as the 6th most planted crop in the world behind wheat, rice, maize, soybean, and barley. The objective of this study was to identify bio-marker among sorghum cultivars using proteomics approach such as two-dimensional polyacrylamide gel electrophoresis (2-DE) coupled with mass spectrometry (MS). METHODS AND RESULTS: Proteins were extracted from sorghum seed, and separated by 2-DE. Total 652 spots were detected from 4 different sorghum seed after staining of 2-DE with colloidal Coomassie brilliant blue (CBB). Among them, 8 spots were differentially expressed and were identified using MALDI-TOF/TOF mass spectrometry. They were involved in RNA metabolism (spot1, spot 4), heat shock proteins (HSPs, spot 2), storage proteins (spot 3, spot 5, and spot 6), and redox related proteins (spot 8). Eight of these proteins were highly up-regulated in Whinchalsusu (WCS). The HSPs, Cupin family protein, and Globulin were specifically accumulated in WCS. The DEAD-box helicase was expressed in 3 cultivars except for WCS. Ribonuclease T2 and aldo-keto reductase were only expressed in 3 cultivars except for Daepung-susu (DPS). CONCLUSION(S): Functions of identified proteins were mainly involved in RNA metabolism, heat shock protein (HSP), and redox related protein. Thus, they may provide new insight into a better understanding of the charactreization between the cultivars of sorghum.

• Korean Journal of Microbiology
• /
• v.54 no.3
• /
• pp.200-207
• /
• 2018

At high salt concentration, glycine betaine is transported into Bacillus subtilis and growing rate of the cell is not suppressed. Also according to recent studies, cell growth is maintained normal growth rate at low temperature. Low temperature results in a stress response of Bacillus subtilis that is characterized by strong repression of major metabolic activities such as translation machinery and membrane transport. In this regards, genes showing cold sensitive phenotype are cold-induced DEAD box RNA helicases (ydbR, yqfR) and fatty acid desaturases (bkdR, des). Therefore to understand the effect of glycine betaine on cold growth of Bacillus subtilis, we investigated the effect of glycine betaine on growth rate of these deletion mutants showing cold sensitive phenotype. Glycine betaine strongly stimulated growth of wild type Bacillus subtilis JH642 and deletion mutants of ydbR and yqfR at $20^{\circ}C$ (190~686 min $T_d$ difference). On the other hands, glycine betaine does not show growth promoting effects on deletion mutants of bkdR, and des at cold conditions. Same cold protectant growth results were shown with the precursor choline instead of glycine betaine. We investigated the effects of detergents on the cell membrane in bkdR and des deficient strains associated with cell membrane. It was identified that bkdR deficient strain shows retarded growth with detergent such as Triton X-100 or N-lauryl sarcosine compared with wild type cell. Thus, it is possible that deletion mutation of bkdR modifies membrane structure and effects on transport of glycine betaine.

• Molecules and Cells
• /
• v.44 no.11
• /
• pp.805-829
• /
• 2021

CCCTC-binding factor (CTCF) critically contributes to 3D chromatin organization by determining topologically associated domain (TAD) borders. Although CTCF primarily binds at TAD borders, there also exist putative CTCF-binding sites within TADs, which are spread throughout the genome by retrotransposition. However, the detailed mechanism responsible for masking the putative CTCF-binding sites remains largely elusive. Here, we show that the ATP-dependent chromatin remodeler, chromodomain helicase DNA-binding 4 (CHD4), regulates chromatin accessibility to conceal aberrant CTCF-binding sites embedded in H3K9me3-enriched heterochromatic B2 short interspersed nuclear elements (SINEs) in mouse embryonic stem cells (mESCs). Upon CHD4 depletion, these aberrant CTCF-binding sites become accessible and aberrant CTCF recruitment occurs within TADs, resulting in disorganization of local TADs. RNA-binding intrinsically disordered domains (IDRs) of CHD4 are required to prevent this aberrant CTCF binding, and CHD4 is critical for the repression of B2 SINE transcripts. These results collectively reveal that a CHD4-mediated mechanism ensures appropriate CTCF binding and associated TAD organization in mESCs.

• Environmental Mutagens and Carcinogens
• /
• v.19 no.1
• /
• pp.28-33
• /
• 1999

The SNF2 family includes proteins from a variety of species with roles I cellular processes such as transcriptional regulation, recombination and various types of DNA repair. Several proteins with unknown function are also included in this family. Here, we report the cloning and characterization of hrp 2+ gene (helicase related gene from S. pombe) which was isolated by PCR amplication using the conserved domain of SNF2 motifs within the ERCC6 gene which encodes a protein involved in DNA excision repair. The hrp2+ gene was isolated by screening with yeast S. pombe genomic library. The isolated cloned contained 6.5 kb insert DNA. Southern blot analysis confirmed that S. pombe chromosome contains the same DNA as hrp2+ gene and this gene exists as a single copy in S. pombe genome. The 4.7 kb transcript of mRNA was identified by Northern blot. To examined the transcriptional regulation of hrp2+ gene, DNA damaging agents were treated. These results indicated that the hrp2+ gene may not be directly involved in DNA replication, but may be involved in damage response pathway.

• Environmental Analysis Health and Toxicology
• /
• v.18 no.4
• /
• pp.287-294
• /
• 2003

출아형 효모 Saccharomyces cerevisiae RAD3 유전자는 절제회복 및 세포의 생존에 필수적이며, DNA dependent ATPase와 DNA-RNA helicase활성을 가지고 있는 것으로 알려져 있다. 본 연구는 분열형 효모 Schizosaccharomyces pombe에서 절제회복과 세포의 생존에 필수적인 출아형 효모 RADS유전자와 유사한 유전자를 S. pombe genomic DNA library에서 분리하여 그 특성을 연구하였다. 분리한 RADS 유사유전자를 HRD3 유전자라 명명하였다. 발현 vector pET3a를 이용하여 분리한 HRD3 유전자를 과 발현하였을 때 HRD3단백질은 숙주단백질의 합성 억제 또는 분해 촉진을 유발하여 숙주세포인 대장균에 독성 효과를 나타냄이 관찰되었다. HRD3유전자와 lacZ유전자를 융합시킨 여러 가지 재조합 vector를 만들어 이들 융합단백질을 분리하였다. 이 결과 HRD3단백질의 카르복실 말단 부위가 DNA회복기능과 대장균에서의 독성효과를 나타내는 중요한 부위로 생각된다.

• Journal of Life Science
• /
• v.17 no.1 s.81
• /
• pp.39-44
• /
• 2007

The Rqh1 gene is essential for vegetative growth in fission Yeast. The rqh1 mutant showed that sensitivity of DNA damaging agent, a wild range of phenotype including abnormal gene expression and cell elongation. This result showed that the rqhl-overexpression cell was sensitivity to DNA damaging agent like rqhl mutant. When Rqh1 have an over-expression by $nmt1^+$ promoter of pREP vector, rqh1 mutant DNA damaging agent sensitivity could be compensated. We isolated two strong mutant containing complementation gene, rqh156 and rqh172, respectively. This result observed that the DNA damaging agent sensitivity of rqhl mutant was complemented by the expression of rqh156 and rqh172. They induced mRNA expression in a dose-dependent manner HU, MMS and UV. The HU sensitivity of the rqhl was complemented by the expression of rqh156 and rqh172. The mRNA expression of rqh156 decreased on HU dose dependent but the mRNA expression of rqh172 did not decrease on HU dose dependent. The MMS and W sensitivity of the rqhl was complemented by the expression of rqh156 and rqh172. These results indicate that the isolated rqhl gene may play an important role in DNA metabolism.

• Animal cells and systems
• /
• v.7 no.2
• /
• pp.159-164
• /
• 2003

The RAD3 gene of Saccharomyces cerevisiae is required for excision repair and is essential for cell viability. The RAD3 encoded protein possesses a single stranded DNA-dependent ATPase and DNA and DNA-RNA helicase activities. To examine the extent of conservation of structure and function of a S. pombe RAD3 during eukaryotic evolution, the RAD3 homolog gene was isolated by screening of genomic DNA library. The isolated gene was designated as HRD3 (homolog of RAD3 gene). Southern blot analysis confirmed that S. pombe chromosome contains the same DNA as HRD3 gene and this gene exists as a single copy in S. pombe. The transcript of 2.8 kb was detected by Northern blot analysis, The level of transcripts increased by ultraviolet (UV) irradiation, indicating that HRD3 is one of the UV-inducible genes in S. pombe. Furthermore, the predicted partial sequence of HRD3 protein has 60％ identity to S. cerevisiae RAD3 gene. This homology was particularly striking in the regions identified as being conserved in a group of DNA helicases. Gene deletion experiments indicate that the HRD3 gene is essential for viability and DNA repair function. These observations suggest evolutionary conservation of other protein components with which HRD3 might interact in mediating its DNA repair and viability functions.

• Genomics & Informatics
• /
• v.16 no.4
• /
• pp.23.1-23.5
• /
• 2018

Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current International Committee on Taxonomy of Viruses taxonomy using an in silico approach, aiming to identify the specific sequence for each virus. We applied this approach to norovirus in Caliciviridae, which causes 90% of gastroenteritis cases worldwide. First, based on the dogma "protein structure determines its function," we hypothesized that the specific sequence can be identified by the specific structure. Firstly, we extracted the coding region (CDS). Secondly, the CDS protein sequences of each genus were annotated by the conserved domain database (CDD) search. Finally, the conserved domains of each genus in Caliciviridae are classified by RPS-BLAST with CDD. The analysis result is that Caliciviridae has sequences including RNA helicase in common. In case of Norovirus, Calicivirus coat protein C terminal and viral polyprotein N-terminal appears as a specific domain in Caliciviridae. It does not include in the other genera in Caliciviridae. If this method is utilized to detect specific conserved domains, it can be used as classification keywords based on protein functional structure. After determining the specific protein domains, the specific protein domain sequences would be converted to gene sequences. This sequences would be re-used one of viral bio-marks.

• Proceedings of the Korean Society of Plant Pathology Conference
• /
• 2003.10a
• /
• pp.125.3-126
• /
• 2003

A near full-length sequence of a new tobamovirus infecting Hibiscus rosa-sinensis L. was determined. The genome consists of 58 nucleotides (nt) 5' UTR, followed by a 4.9 kb ORF which methyl transferase helicase domain (128 kDa), readthrough protein RNA dependent RNA polymerase (RdRp) 185 kDa and a 52 kDa protein. The 128 kDa protein had a maximum homology of 51.4 ％ to TMGMV and amino acids (an) were 54.3 ％ identical to TMV- vulgare strain. The 185 kDa RdRp had a maximum homology of 53.5％ to TMV-Ob and KGMMV-Y and a 59.6％ homology at the an level to CGMMV-SH. The MP gene encodes 282 aa and its theoretical molecular weight is 30.4 kDa. The nt and an sequence identities of MP ranged from 38.8％ to 43.9％ and 30.9％ to 37.9％, respectively. The CP gene encodes 163 residues and with a theoretical molecular weight of 18.2 kDa The (nt) and aa sequences of the CP were 46.9 ％ to 51.6％ and 45.3％ to 57.1％ identical to other tobamoviruses, respectively. The predicted virion origin of assembly (OAS) was located in the CP gene. Phylogenetic trees generated based on the nt and as sequences of RdRp, MP and CP genes indicated that this new virus clustered with subgroup II tobamoviruses. Although the CP ORF of this virus shared a high nt and aa sequence identity with Sunn-hemp mosaic virus (SHMV), Western analysis showed that it is serologically unrelated to SHMV. We propose the name Hibiscus virus S (HVS) for this Singapore isolate. This is the first report on a near full-length sequence of a Tobamovirus that infects hibiscus.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.11
• /
• pp.1833-1840
• /
• 2007

Viruses in garlic plants (Allium sativum L.) have accumulated and evolved over generations, resulting in serious consequences for the garlic trade around the world. These viral epidemics are also known to be caused by aphids and eriophyid mites (Aceria tulipae) carrying Potyviruses, Carlaviruses, and Allexiviruses. However, little is known about viral epidemics in garlic plants caused by eriophyid mites. Therefore, this study investigated the infection of garlic plants with Allexiviruses by eriophyid mites. When healthy garlic plants were cocultured with eriophyid mites, the leaves of the garlic plants developed yellow mosaic strips and became distorted. In extracts from the eriophyid mites, Allexiviruses were observed using immunosorbent electron microscopy (ISEM). From an immunoblot analysis, coat proteins against an Allexivirus garlic-virus antiserum were clearly identified in purified extracts from collected viral-infected garlic plants, eriophyid mites, and garlic plants infected by eriophyid mites. A new strain of GarV-B was isolated and named GarV-B Korea isolate 1 (GarV-B1). The ORF1 and ORF2 in GarV-B1 contained a typical viral helicase, RNA-directed RNA polymerase (RdRp), and triple gene block protein (TGBp) for viral movement between cells. The newly identified GarV-B1 was phylogenetically grouped with GarV-C and GarV-X in the Allexivirus genus. All the results in this study demonstrated that eriophyid mites are a transmitter insect species for Allexiviruses.