• Genomics & Informatics
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• v.21 no.3
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• pp.36.1-36.19
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• 2023

The LIM domain-containing proteins are dominantly found in plants and play a significant role in various biological processes such as gene transcription as well as actin cytoskeletal organization. Nevertheless, genome-wide identification as well as functional analysis of the LIM gene family have not yet been reported in the economically important plant sorghum (Sorghum bicolor L.). Therefore, we conducted an in silico identification and characterization of LIM genes in S. bicolor genome using integrated bioinformatics approaches. Based on phylogenetic tree analysis and conserved domain, we identified five LIM genes in S. bicolor (SbLIM) genome corresponding to Arabidopsis LIM (AtLIM) genes. The conserved domain, motif as well as gene structure analyses of the SbLIM gene family showed the similarity within the SbLIM and AtLIM members. The gene ontology (GO) enrichment study revealed that the candidate LIM genes are directly involved in cytoskeletal organization and various other important biological as well as molecular pathways. Some important families of regulating transcription factors such as ERF, MYB, WRKY, NAC, bZIP, C2H2, Dof, and G2-like were detected by analyzing their interaction network with identified SbLIM genes. The cis-acting regulatory elements related to predicted SbLIM genes were identified as responsive to light, hormones, stress, and other functions. The present study will provide valuable useful information about LIM genes in sorghum which would pave the way for the future study of functional pathways of candidate SbLIM genes as well as their regulatory factors in wet-lab experiments.

• IMMUNE NETWORK
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• v.20 no.5
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• pp.36.1-36.13
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• 2020

Hippo signaling pathways are evolutionarily conserved signal transduction mechanisms mainly involved in organ size control, tissue regeneration, and tumor suppression. However, in mammals, the primary role of Hippo signaling seems to be regulation of immunity. As such, humans with null mutations in STK4 (mammalian homologue of Drosophila Hippo; also known as MST1) suffer from recurrent infections and autoimmune symptoms. Although dysregulated T cell homeostasis and functions have been identified in MST1-deficient human patients and mouse models, detailed cellular and molecular bases of the immune dysfunction remain to be elucidated. Although the canonical Hippo signaling pathway involves transcriptional co-activator Yes-associated protein (YAP) or transcriptional coactivator with PDZ motif (TAZ), the major Hippo downstream signaling pathways in T cells are YAP/TAZ-independent and they widely differ between T cell subsets. Here we will review Hippo signaling mechanisms in T cell immunity and describe their implications for immune defects found in MST1-deficient patients and animals. Further, we propose that mutual inhibition of Mst and Akt kinases and their opposing roles on the stability and function of forkhead box O and β-catenin may explain various immune defects discovered in mutant mice lacking Hippo signaling components. Understanding these diverse Hippo signaling pathways and their interplay with other evolutionarily-conserved signaling components in T cells may uncover molecular targets relevant to vaccination, autoimmune diseases, and cancer immunotherapies.

• Journal of Microbiology and Biotechnology
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• v.33 no.12
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• pp.1595-1605
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• 2023

Dehydroquinate dehydratase (DHQD) catalyzes the conversion of 3-dehydroquinic acid (DHQ) into 3-dehydroshikimic acid in the mid stage of the shikimate pathway, which is essential for the biosynthesis of aromatic amino acids and folates. Here, we report two the crystal structures of type II DHQD (CgDHQD) derived from Corynebacterium glutamicum, which is a widely used industrial platform organism. We determined the structures for CgDHQD^WT with the citrate at a resolution of 1.80Å and CgDHQD^R19A with DHQ complexed forms at a resolution of 2.00 Å, respectively. The enzyme forms a homododecamer consisting of four trimers with three interfacial active sites. We identified the DHQ-binding site of CgDHQD and observed an unusual binding mode of citrate inhibitor in the site with a half-opened lid loop. A structural comparison of CgDHQD with a homolog derived from Streptomyces coelicolor revealed differences in the terminal regions, lid loop, and active site. Particularly, CgDHQD, including some Corynebacterium species, possesses a distinctive residue P105, which is not conserved in other DHQDs at the position near the 5-hydroxyl group of DHQ. Replacements of P105 with isoleucine and valine, conserved in other DHQDs, caused an approximately 70% decrease in the activity, but replacement of S103 with threonine (CgDHQD^S103T) caused a 10% increase in the activity. Our biochemical studies revealed the importance of key residues and enzyme kinetics for wild type and CgDHQD^S103T, explaining the effect of the variation. This structural and biochemical study provides valuable information for understanding the reaction efficiency that varies due to structural differences caused by the unique sequences of CgDHQD.

• Journal of Marine Bioscience and Biotechnology
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• v.16 no.1
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• pp.1-18
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• 2024

Coastal dunes must be conserved. Their native halophytes support coastal geography while their symbiotic microorganisms help vegetation thrive. The Goraebul coast has the largest, well-conserved dune system on the East Sea of the Korean Peninsula due to a climax mixed halophyte (C. soldanella, C. kobomugi, and E. mollis) vegetation support. This study identified rhizobacteria and their diversity in mixed halophyte communities unique to Goraebul. Five phyla, 12 genera, and 21 species were identified based on 16S rDNA sequences from 65 isolates. The phylum Bacillota, class Bacillota, order Bacillales, and family Bacillaceae were identified, with Bacillus as the dominant genus (46.15%). The richness and Shannon's diversity were higher at the species than at the genus level due to the dominance of Bacillus; however, various Bacillus species (7) were identified. Therefore, the climax mixed vegetation adapted to the Goraebul coast may exert natural selection pressure in favor of the common characteristics of Bacillus. However, despite this advantage, the Shannon equitability (0.86), Simpson (0.08), and Shannon diversity (2.79) indexes indicate a stable rhizosphere cluster and the climax mixed vegetation is affected by symbiotic relationships between healthy rhizosphere microbiota.

• Journal of Microbiology and Biotechnology
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• v.34 no.6
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• pp.1276-1286
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• 2024

The environment has been identified as an origin, reservoir, and transmission route of antibiotic resistance genes (ARGs). Among diverse environments, freshwater environments have been recognized as pivotal in the transmission of ARGs between opportunistic pathogens and autochthonous bacteria such as Aeromonas spp. In this study, five environmental strains of Aeromonas spp. exhibiting multidrug resistance (MDR) were selected for whole-genome sequencing to ascertain their taxonomic assignment at the species-level and to delineate their ARG repertoires. Analyses of their genomes revealed the presence of one protein almost identical to AhQnr (A. hydrophila Qnr protein) and four novel proteins similar to AhQnr. To scrutinize the classification and taxonomic distribution of these proteins, all Aeromonas genomes deposited in the NCBI RefSeq genome database (1,222 genomes) were investigated. This revealed that these Aeromonas Qnr (AQnr) proteins are conserved intrinsic resistance determinants of the genus, exhibiting species-specific diversity. Additionally, structure prediction and analysis of contribution to quinolone resistance by AQnr proteins of the isolates, confirmed their functionality as quinolone resistance determinants. Given the origin of mobile qnr genes from aquatic bacteria and the crucial role of Aeromonas spp. in ARG dissemination in aquatic environments, a thorough understanding and strict surveillance of AQnr families prior to the clinical emergence are imperative. In this study, using comparative genome analyses and functional characterization of AQnr proteins in the genus Aeromonas, novel Aeromonas ARGs requiring surveillance has suggested.

• Archives of Pharmacal Research
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• v.21 no.6
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• pp.634-639
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• 1998

Seven transmembrane segment (7TMS) receptors for chemokines and related molecules have been demonstrated to be essential, in addition to CD4, for HIV and SIV infection. The beta-chemokine receptor CCR5 is the primary, perhaps sole, coreceptor for HIV-1 during the early and chronic phases of infection, and supports infection by most primary HIV-1 and many SIV isolates. Late-stage primary and laboratory-adapted HIV-1, HIV-2, and SIV isolates can use other 7TMS receptors. CXCR4 appears especially important in late-stage HIV infection; several related receptors can also be used. The specificity of SIV viruses is similar. Commonalities among these receptors, combined with analyses of mutated molecules, indicate that discrete, conformationally-depenclent sites on the chemokine receptors determine their association with the third variable and conserved regions of viral envelope glycoproteins. These studies are useful for elucidating the mechanism and molecular determinants of HIV-1 entry, and of inhibitors to that entry.

• Journal of Microbiology
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• v.44 no.6
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• pp.617-621
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• 2006

Coprinellus congregatus secreted a laccase isozyme when the culture was transferred to an acidic liquid medium (pH 4.1). The laccase cDNA gene (clac2) was used as a probe for cloning of the genomic laccase gene (lac2) including the promoter (Plac2). The open reading frame (ORF) of lac2 had 526 deduced amino acids and four conserved copper binding domains as other fungal laccases. Recombinant plasmid (pRSlac2p-cDNA) of lac2 cDNA with its own promoter was transformed in Saccharomyces cerevisiae. Expression of the transformed lac2 gene was induced by oxidative stress ($H_2O_2$) in yeast and the survival rate of the transformed yeast strain was greatly increased when compared with that of the control strain transformed with pRS316 yeast vector.

• Journal of Photoscience
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• v.9 no.2
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• pp.17-20
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• 2002

We have cloned a cDNA for an opsin (Boceropsin) from the silkworm larval brain which was suggested to contain the photoperiodic receptor. Its deduced amino acid sequence was composed of 381 amino acids and included amino acid residues highly conserved in insect visual pigments. This opsin belonged to the long wavelength photoreceptor group of insect opsins, and are presumed to be photoperiodic receptor. RT-PCR analysis revealed that Boceropsin mRNA is expressed in the larval brain, but not in the subesophageal (Sg) and thoracic ganglion. Immunohistochemical analyses demonstrated that Boceropsin protein is present bilaterally in some defined cells localized in the brain of the Bombyx larva. Boceropsin was considered not to be involved in the circadian photoreception, because carotenoids are not indispensable for the photoreception and formation of circadian rhythms in the silkworm.

• Journal of Ginseng Research
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• v.21 no.3
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• pp.147-152
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• 1997

Ginsenosides $Rh_1$ and $Rh_2$ Induced the differentiation of F9 teratocarcinoma stem cells. These agents are structurally similar to the steroid hormones, therefore, we speculated that the steroid receptor (s) or novel nuclear receptor (s) could be involved in the differentiation process induces by them. Based on this speculation, we tried to alone new nuclear receptors with reverse transcription-polymerase chain reaction (RT-PCR) method by isolating RNA from F9 teratocarcinoma cells induced by ginsenosides. By using RT-PCR with degenerated primers from highly conserved DNA binding domain of nuclear receptors, we identified several nuclear receptors. In northern blot analysis we found that these clones are transcriptionally regulated by ginsenoside Rhl or Rh2 treatment. Further characterizations of these clones are needed to identify the mechanism of gene expression, which has an important role in the differentiation of F9 cells induced by ginsenosides.

• Korean Journal of Plant Resources
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• v.25 no.6
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• pp.739-744
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• 2012

The plant Empetrum nigrum, valued in the traditional system of medicine, is well known for its antibacterial, antifungal, and antioxidant properties. In the present work, the effect of removal of shoot apical meristem (SAM) on shoot proliferation was studied. It was observed that removal of SAM promoted shoot proliferation whereas intact tip resulted in higher survival percentage. Further, the effect of different concentrations of BA on above was also studied. During root formation the effect of light quality after treatment with IBA was investigated. For rooting, continuous red light without IBA resulted in maximum rooting percentage. The above factors when taken into consideration during micropropagation of this endangered plant can result in healthier plantlets. The results show that the species could be successfully conserved by in vitro propagation system.