• Animal cells and systems
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• v.9 no.3
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• pp.139-144
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• 2005

The attractant (orange light) or repellent (white light) signal is transmitted from SRI (Sensory Rhodopsin I) via protein-protein interaction with its transducer Htrl (Halobacterial Transducer for Sensory Rhodopsin I) which in turn controls a cytoplasmic phospho-transfer pathway that modulates flagella motor switching in Halobacterium salinarum. Some mutations in both SRI and Htrl showed an unusual mutant phenotype called inverted signaling, in which the cell produces a repellent response to normally attractant light. Twelve mutations at the Glutamate 56 (E56) position in the second transmembrane helix of Htrl were introduced by site-specific random mutagenesis. Almost all E56 mutants showed orange-light inverted responses in pH and temperature-dependent manners except E56D and E56Y. Except for these two mutants, all mutants accelerated the $S_{373}$ decay compared to wild-type at $18^{\circ}C$. This supported that there is an interaction between SRI and the second transmembrane of Htrl. Also a structural model of Htrl based on the Tar crystal structure and the secondary structure prediction program proposed the E56 residue to be in the middle of the proton channel. The most important observation is that the E56 mutant provides the evidence that this residue is very sensitive for signal relay, which can be explained by the open and closed conformations of the channel (A and R conformations) in SRI, as was postulated by the unified conformational shuttling model for transport and signaling.

• Molecules and Cells
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• v.22 no.3
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• pp.328-335
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• 2006

Imperatoxin A ($IpTx_a$), a 3.7 kDa peptide from the African scorpion Pandinus imperator, is an agonist of the skeletal muscle ryanodine receptor (RyR1). In order to study the structure of the toxin and its effect on RyR1, $IpTx_a$ cDNA was PCR-amplified using 3 pairs of primers, and the toxin was expressed in E. coli. The toxin was further purified by chromatography, and various point mutants in which basic amino acids were substituted by alanine were prepared by site-directed mutagenesis. Studies of single channel properties by the planar lipid bilayer method showed that the recombinant $IpTx_a$ was identical to the synthetic $IpTx_a$ with respect to high-performance liquid chromatography mobility, amino acid composition and specific effects on RyR1. Mutations of certain basic amino acids ($Lys^{19}$, $Arg^{23}$, and $Arg^{33}$) dramatically reduced the capacity of the peptide to activate RyRs. A subconductance state predominated when $Lys^8$ was substituted with alanine. These results suggest that some basic amino acid residues in $IpTx_a$ are important for activation of RyR1, and that $Lys^8$ plays an important role in regulating the gating mode of RyR1.

• Molecules and Cells
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• v.44 no.10
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• pp.723-735
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• 2021

Spemann organizer is a center of dorsal mesoderm and itself retains the mesoderm character, but it has a stimulatory role for neighboring ectoderm cells in becoming neuroectoderm in gastrula embryos. Goosecoid (Gsc) overexpression in ventral region promotes secondary axis formation including neural tissues, but the role of gsc in neural specification could be indirect. We examined the neural inhibitory and stimulatory roles of gsc in the same cell and neighboring cells contexts. In the animal cap explant system, Gsc overexpression inhibited expression of neural specific genes including foxd4l1.1, zic3, ncam, and neurod. Genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) and promoter analysis of early neural genes of foxd4l1.1 and zic3 were performed to show that the neural inhibitory mode of gsc was direct. Site-directed mutagenesis and serially deleted construct studies of foxd4l1.1 promoter revealed that Gsc directly binds within the foxd4l1.1 promoter to repress its expression. Conjugation assay of animal cap explants was also performed to demonstrate an indirect neural stimulatory role for gsc. The genes for secretory molecules, Chordin and Noggin, were up-regulated in gsc injected cells with the neural fate only achieved in gsc uninjected neighboring cells. These experiments suggested that gsc regulates neuroectoderm formation negatively when expressed in the same cell and positively in neighboring cells via soluble factors. One is a direct suppressive circuit of neural genes in gsc expressing mesoderm cells and the other is an indirect stimulatory circuit for neurogenesis in neighboring ectoderm cells via secreted BMP antagonizers.

• Molecules and Cells
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• v.42 no.2
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• pp.123-134
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• 2019

Lysophosphatidic acid (LPA) is an endogenous lysophospholipid with signaling properties outside of the cell and it signals through specific G protein-coupled receptors, known as $LPA_{1-6}$. For one of its receptors, $LPA_1$ (gene name Lpar1), details on the cis-acting elements for transcriptional control have not been defined. Using 5'RACE analysis, we report the identification of an alternative transcription start site of mouse Lpar1 and characterize approximately 3,500 bp of non-coding flanking sequence 5' of mouse Lpar1 gene for promoter activity. Transient transfection of cells derived from mouse neocortical neuroblasts with constructs from the 5' regions of mouse Lpar1 gene revealed the region between -248 to +225 serving as the basal promoter for Lpar1. This region also lacks a TATA box. For the region between -761 to -248, a negative regulatory element affected the basal expression of Lpar1. This region has three E-box sequences and mutagenesis of these E-boxes, followed by transient expression, demonstrated that two of the E-boxes act as negative modulators of Lpar1. One of these E-box sequences bound the HeLa E-box binding protein (HEB), and modulation of HEB levels in the transfected cells regulated the transcription of the reporter gene. Based on our data, we propose that HEB may be required for a proper regulation of Lpar1 expression in the embryonic neocortical neuroblast cells and to affect its function in both normal brain development and disease settings.

• Journal of Life Science
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• v.20 no.9
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• pp.1332-1338
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• 2010

To elucidate the mechanism underlying the regulation of hST8Sia I gene expression in FenR-induced SH-SY5Y cells, we characterized the promoter region of the hST8Sia I gene. Functional analysis of the 5'-flanking region of the hST8Sia I gene showed that the -1146 to -646 region functions as the FenR-inducible promoter of hST8Sia I in SH-SY5Y cells. Site-directed mutagenesis indicated that the NF-&B binding site at -731 to -722 was crucial for the FenR-induced expression of hST8Sia I in SH-SY5Y cells. To investigate which signal transduction pathway was involved in FenR-stimulated induction of hST8Sia I in SH-SY5Y cells, we performed Western blot analysis using phospho-specific antibodies in order to measure their degree of regulatory phosphorylation. Phosphorylations of AKT and RelA (p65) subunit of NF-${\kappa}B$ were significantly elevated in cytosolic and nuclear fractions of FenR-stimulated SH-SY5Y cells, respectively, than in control or DMSO-treated SH-SY5Y cells. These results suggest that FenR induce transcriptional up-regulation of hST8Sia I gene expression through translocation of RelA (p65) subunit of NF-${\kappa}B$ to nucleus by AKT signal pathway in SH-SY5Y cells.

• Korean Journal of Microbiology
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• v.52 no.4
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• pp.455-462
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• 2016

Pseudomonas aeruginosa P-5 is an unusual organism capable of synthesizing polyhydroxyalkanoates (PHAs) consisting of 3-hydroxyvalerate (3HV) and medium-chain-length (MCL) 3-hydroxyalkanoate (3HA) monomer units when C-odd alkanoic acids are fed as the sole carbon source. Evaluation of the substrate chain-length specificity of two P. aeruginosa P-5 PHA synthases ($PhaC1_{P-5}$ and $PhaC2_{P-5}$) by heterologous expression of $PhaC1_{P-5}$ and $PhaC2_{P-5}$ genes in Pseudomonas putida GPp104 revealed that $PhaC2_{P-5}$ incorporates both 3HV and MCL 3HAs into PHA, whereas $PhaC1_{P-5}$ favors only MCL 3HAs for polymerization. In order to obtain $PhaC2_{P-5}$ mutants with altered substrate specificity, site-specific mutagenesis for $PhaC2_{P-5}$ was conducted. Amino acid substitutions of $PhaC2_{P-5}$ at two positions (Ser326Thr and Gln482Lys) were very effective for synthesizing copolymers with a higher 3HV fraction. When recombinant P. putida GPp104 harboring double mutated $phaC2_{P-5}$ gene ($phaC2_{P-5}QKST$) was grown on nonanoic acid, 2.5-fold increase of copolymer content with 3.8-fold increase of 3HV fraction was observed. The $phaC2_{P-5}QKST$-containing Ralstonia eutropha PHB-4 supplemented with valeric acid also produced copolymers consisting of 3HV and 3-hydroxyheptanoate with a high 3HV fraction. These results suggest that recombinants containing $phaC2_{P-5}QKST$ could be useful for production of new PHA copolymers with improved material properties.

• Molecules and Cells
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• v.25 no.1
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• pp.30-42
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• 2008

The disease-specific (dsp) region and the hypersensitive response and pathogenicity (hrp) genes, including the hrpW, $hrpN_{Ep}$, and hrpC operons have previously been sequenced in Erwinia pyrifoliae WT3 [Shrestha et al. (2005a)]. In this study, the remaining hrp genes, including the hrpC, hrpA, hrpS, hrpXY, hrpL and hrpJ operons, were determined. The hrp genes cluster (ca. 38 kb) was comprised of eight transcriptional units and contained nine hrc (hrp conserved) genes. The genetic organization of the hrp/hrc genes and their orientation for the transcriptions were also similar to and collinear with those of E. amylovora, showing ${\geq}80%$ homologies. However, ORFU1 and ORFU2 of unknown functions, present between the hrpA and hrpS operons of E. amylovora, were absent in E. pyrifoliae. To determine the HR active domains, several proteins were prepared from truncated fragments of the N-terminal and the C-terminal regions of $HrpN_{Ep}$ protein of E. pyrifoliae. The proteins prepared from the N-terminal region elicited HR, but not from those of the C-terminal region indicating that HR active domains are located in only N-terminal region of the $HrpN_{Ep}$ protein. Two synthetic oligopeptides produced HR on tobacco confirming presence of two HR active domains in the $HrpN_{Ep}$. The HR positive N-terminal fragment ($HN{\Delta}C187$) was further narrowed down by deleting C-terminal amino acids and internal amino acids to investigate whether amino acid insertion region have role in faster and stronger HR activity in $HrpN_{Ep}$ than $HrpN_{Ea}$. The $HrpN_{Ep}$ mutant proteins $HN{\Delta}C187$ (D1AIR), $HN{\Delta}C187$ (D2AIR) and $HN{\Delta}C187$ (DM41) retained similar HR activation to that of wild-type $HrpN_{Ep}$. However, the $HrpN_{Ep}$ mutant protein $HN{\Delta}C187$ (D3AIR) lacking third amino acid insertion region (102 to 113 aa) reduced HR when compared to that of wild-type $HrpN_{Ep}$. Reduction in HR elicitation could not be observed when single amino acids at different positions were substituted at third amino acids insertion region. But, substitution of amino acids at L103R, L106K and L110R showed reduction in HR activity on tobacco suggesting their importance in activation of HR faster in the $HrpN_{Ep}$ although it requires further detailed analysis.

• Molecules and Cells
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• v.39 no.8
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• pp.594-602
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• 2016

Alkyl hydroperoxide reductase subunit C from Pseudomonas aeruginosa PAO1 (PaAhpC) is a member of the 2-Cys peroxiredoxin family. Here, we examined the peroxidase and molecular chaperone functions of PaAhpC using a site-directed mutagenesis approach by substitution of Ser and Thr residues with Cys at positions 78 and 105 located between two catalytic cysteines. Substitution of Ser with Cys at position 78 enhanced the chaperone activity of the mutant (S78C-PaAhpC) by approximately 9-fold compared with that of the wild-type protein (WT-PaAhpC). This increased activity may have been associated with the proportionate increase in the high-molecular-weight (HMW) fraction and enhanced hydrophobicity of S78C-PaAhpC. Homology modeling revealed that mutation of $Ser^{78}$ to $Cys^{78}$ resulted in a more compact decameric structure than that observed in WT-PaAhpC and decreased the atomic distance between the two neighboring sulfur atoms of $Cys^{78}$ in the dimer-dimer interface of S78C-PaAhpC, which could be responsible for the enhanced hydrophobic interaction at the dimer-dimer interface. Furthermore, complementation assays showed that S78C-PaAhpC exhibited greatly improved the heat tolerance, resulting in enhanced1 survival under thermal stress. Thus, addition of Cys at position 78 in PaAhpC modulated the functional shifting of this protein from a peroxidase to a chaperone.

• KSBB Journal
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• v.16 no.2
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• pp.188-199
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• 2001

A gene encoding the dextransucrase(dsCB) that synthesizes mostly $\alpha-(1\rightarrow6)$ linked dextran with low amount(10%) of $\alpha-(1\rightarrow3)$ branching was cloned and sequenced from Leuconostoc mesenteroides B-742CB. The 6.1 kbp DNA fragment carrying dsCB showed one open reading frame(ORF) composed of 4,536bp. The deduced amino acid sequence shows that it begins from the start codon(ATG) at position 698 of the cloned DNA fragment and extends to the termination condon(TAA) at position 5,223. The enzyme is consisted of 1,508 amino acids and has an calculated molecular mass of 168.6kDa. This calculated Mw was in good agreement with an activity band of 170kDa on non-denaturing SDS-PAGE. A recombinant E. coli DH5 $alpha$ harboring pDSCB produced extracellular dextransucrase in 2% sucrose medium, and synthesized both soluble and insoluble dextran. To compare the properties of enzyme with B-742CB dextransucrase, the acceptor reaction, hydrolysis of dextran and methylation were performed. The expressed enzyme showed the same properties as B-742CB dextransucrease, but its ability to synthesize $\alpha-(1\rightarrow3)$ branching was lower than that of B-742CB dextransucrase. In order to identify the critical amino acid residues known as conserved regions related to catalytic activity, Asp-492 was replaced with Asn. D492N resulted in a 1.6 fold decrease in specific activity.

• Korean Journal of Microbiology
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• v.32 no.2
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• pp.102-108
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• 1994

Autonomously replicating sequence Binding Factor 1(ABF1) is a DNA-binding protein that specifically recognizes the $RTCRYN_5ACG$ at many sites in the yeast genome including the promoter element, mating-type silencer and ARS. To express the intact full-length ABF1 gene in E. coli, the ABF1 gene has been cloned into pMAL-c2 and His-61, Leu-353 and Leu-360 were substituted with other amino acid. ABF1 fusion proteins of wild type ABF1 and H61A, L353R and L360R nutants were purified by amylose resin affinity chromatography. Fusion protein of MBP and ABF1 was digested by Factor Xa and Characterized by gel retardation assay and complementation test. As aresult, we suggested that other DNA binding motif except atypical inc-finger motif is in the middle region of ABF1.