• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.7-11
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• 2007

Methods for making scoring matrix based on phylogenetic tree for all possible exchanges of one amino acid with another. PFMT(Phylogenetic focused Mutation Tendency) matrix is different BLOSUM62 and PAM160 which are the most used scoring matrixes. This matrix calculates possibility of substitution from common ancestor to high spices. PFMT matrix scores substitution frequency in COGs databases which contain 152 KOGs's dataset. PFMT matrix usefully is able to compare between query sequence and sequences of more higher species and show detailed substitution relation of 20 amino acids.

• Animal cells and systems
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• v.10 no.4
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• pp.197-201
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• 2006

Diaminopimelate decarboxylase (DAPDC, EC 4.1.1.20) catalyzes the conversion of diaminopimelate into lysine (Lys), which is the last step in Lys biosynthetic pathway. The genes for DAPDC have been reported in many bacteria, and more recently in Arabidopsis. Here we report characterization of a gene for DAPDC from rice (OsDAPDC). Sequence analysis of a cDNA clone revealed a full-length open reading frame for OsDAPDC that encoded 490 amino acids, approximately 53.2 kDa protein. The OsDAPDC protein contains a consensus binding site for pyridoxal-5'-phosphate as a cofactor and has a sequence at the amino terminus that resembles a transit peptide for localization to plastids, similar to that of Arabidopsis. Single gene encoding DAPDC was found in chromosome II in rice. The predicted amino acid sequence of OsDAPDC is highly homologous to that of the enzymes for DAPDC encoded by lysA of many bacteria. Expression of OsDAPDC in lysA mutants of Escherichia coli shows that the gene is able to functionally complement the mutants. These results suggest that OsDAPDC encodes a protein for diaminopimelate decarboxylase in rice.

• Journal of Microbiology and Biotechnology
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• v.18 no.7
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• pp.1235-1244
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• 2008

Indole-3-acetic acid (IAA) is produced commonly by plants and many bacteria, however, little is known about the genetic basis involving the key enzymes of IAA biosynthetic pathways from Bacillus spp. IAA intermediates from the Gram-positive spore-forming bacterium Paenibacillus polymyxa E681 were investigated, which showed the existence of only an indole-3-pyruvic acid (IPA) pathway for IAA biosynthesis from the bacterium. Four open reading frames (ORFs) encoding indole-3-pyruvate decarboxylase-like proteins and putative indole-3-pyruvate decarboxylase (IPDC), a key enzyme in the IPA synthetic pathway, were found on the genome sequence database of P. polymyxa and cloned in Escherichia coli DH5$\alpha$. One of the ORFs, PP2_01257, was assigned as probable indole-3-pyruvate decarboxylase. The ORF consisted of 1,743 nucleotides encoding 581 amino acids with a deduced molecular mass of 63,380 Da. Alignment studies of the deduced amino acid sequence of the ORF with known IPDC sequences revealed conservation of several amino acids in PP2_01257, essential for substrate and cofactor binding. Recombinant protein, gene product of the ORF PP2_01257 from P. polymyxa E681, was expressed in E. coli BL21 (DE3) as a glutathione S-transferase (GST)-fusion protein and purified to homogeneity using affinity chromatography. The molecular mass of the purified enzyme showed about 63 kDa, corresponding closely to the expected molecular mass of IPDC. The indole-3-pyruvate decarboxylase activity of the recombinant protein, detected by HPLC, using IPA substrate in the enzyme reaction confirmed the identity and functionality of the enzyme IPDC from the E681 strain.

• Parasites, Hosts and Diseases
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• v.35 no.2
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• pp.105-110
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• 1997

The gene encoding the 33 kDa piroplasm surface protein of Theileria sergenti isolated in Korea was cloned and the nucleotide sequence was determined by dideoxy chaill termination method. The cloned gene corresponds to 869 bps encoding an open reading frame of 283 amino acids. Comparison of the sequence between Korean and .Tapanese isolates showed 99.4% homology rate in the nucleotide sequence and 98.9% homology rate in the amino acid sequence.

• Journal of Microbiology and Biotechnology
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• v.9 no.4
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• pp.404-413
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• 1999

Methanopyrus kandleri is a hyperthermophilic methanogen that represents one of the most heat-resistant organisms: the maximum growth temperature of M. kandleri is $110^{\circ}C$. A random sequence analysis of the genomic DNA of M. kandleri has been performed to obtain genomic information. More than 200 unique sequence tags were obtained and compared with the sequences in the GenBank and PIR databases. About 30% of the analyzed tags showed strong sequence similarity to previously identified genes involved in various cellular processes such as biosynthesis, transport, methanogenesis, or metabolism. When statistics relating to the frequency of codons were examined, the sequenced open reading frames showed highly biased codon usage and a high content of charged amino acids. Among the identified genes, a homologue of the catalytic subunit of carbon monoxide dehydrogenase (CODH) that reduces $CO_2$ to CO was cloned and sequenced in order to examine its detailed gene structure. The cloned gene includes consensus promoters. The amino acid sequence of the cloned gene shows a strong homology with the CODH genes from methanogenic Archaea, especially in the presumed binding sites for Fe-S centers.

• Preventive Nutrition and Food Science
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• v.15 no.4
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• pp.360-363
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• 2010

To enhance the expression and secretion of pediocin PA-1 from heterologous bacterial hosts, the promoter and deduced signal sequence (PS) of an $\alpha$-amylase gene from a Bifidobacterium adolescentis strain was fused with pediocin PA-1 structural and immunity genes (AB) and the resulting functions were evaluated in Escherichia coli. Two recombinant PCR products were created-one with just the deduced signal sequence and one with the sequence plus the Ser and Thr sequences that are the next two amino acids of the signal sequence. These two products, the PSAB (---AQA::KYY---) and PSABST (---AQA$\underline{ST}$::KYY---), respectively, were inserted into a TA cloning vector (yT&A) and named pPSAB, which was previously reported, and pPSABST. The two recombinant plasmid DNAs were transferred into E. coli JM109 and the transformants displayed antimicrobial activity, where the activity of E. coli JM109 (pPSAB) was stronger than that of E. coli JM109 (pPSABST), indicating that the ST amino acid residues were not necessary for secretion and might have even decreased the antimicrobial activity of recombinant pediocin PA-1.

• Journal of Microbiology and Biotechnology
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• v.11 no.3
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• pp.443-451
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• 2001

In order to investigate what kind of response anaerobic bifidobacteria has on oxygen stress, five oxygen-tolerant bifidobacteria were isolated from human fecal samples. All were temporarily identified as Bifidobacterium longum through an analysis of carbohydrate utilization patterns and cellular fatty acid profiles. In the presence of oxygen, the lag phase became extended and the cell growth was suppressed. Bifidobacterial cell was able to remove dissolved oxygen in an early stage of growth and to overcome oxygen stress to a certain extent. The cell became long n size and showed a rough surface containing many nodes which were derived from abnormal or incomplete cell division. Cellular fatty acid profiled changed remarkably under a partially aerobic condition, so that the carbon chain of cellular fatty acid became short. All the dimethyl acetals originated from plasmalogen were reduced, any cyclopropane fatty acid, 9, 10-methyleneoctadecanoic acid ($C_{19:0}cyc9,10$), was increased remarkably. Oxygen stress induced a 5.5 kD protein in B. longum JI 1 of the oxygen-teolerant bifidobacteria, that was named Osp protein, and its N-terminal amino acid sequence was as follows: unknown amino acid-Thr-Gly-Val-Arg-Phe-Ser-Asp-Asp-Glu. Therefore, the oxygen-tolerant bifidobacteria seemed to defend against oxygen stress byincreasing the content of short fatty acid and cyclopropane fatty acid, and induction of an oxygen stress protein, but not the plasmalogen.

• Journal of Microbiology and Biotechnology
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• v.20 no.4
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• pp.670-677
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• 2010

An alkaline pectate lyase, Bsp165PelA, was purified to homogeneity from the culture broth of alkaliphilic Bacillus sp. N16-5. The enzyme showed a specific activity as high as 1,000 U/mg and had optimum activity at pH 11.5 and $50^{\circ}C$. It was composed of a single polypeptide chain with a molecular mass of 42 kDa deduced from SDS-PAGE, and its isoelectric point was around pH 6.0. It could efficiently depolymerize polygalacturonate and pectin. Characterization of product formation revealed unsaturated digalacturonate and trigalacturonate as the main products. The pectate lyase gene (pelA) contained an open reading frame (ORF) of 1,089 bp, encoding a 36-amino acids signal peptide and a mature protein of 326 amino acids with a calculated molecular mass of 35.943 Da. The deduced amino acid sequence from the pelA ORF exhibited significant homology to those of known pectate lyases in polysaccharide lyase family 1. Some conserved active-site amino acids were found in the deduced amino acid sequence of Bsp165PelA. $Ca^{2+}$ was not required for activity on pectic substrates.

• Journal of Microbiology
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• v.42 no.3
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• pp.188-193
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• 2004

Xanthobacter flavus strain UE15 was isolated in wastewater obtained from the Ulsan industrial complex, Korea. This strain functions as a 1,2-dichloroethane (1,2-DCA) degrader, via a mechanism of hydrolytic dechlorination, under aerobic conditions. The UE15 strain was also capable of dechlorinating other chloroaliphatics such as 2-chloroacetic acid and 2-chloropropionic acid. The dhlA gene encoding 1,2-DCA dechlorinase was cloned from the genomic DNA of the UE15 strain, and its nucleotide sequence was determined to consist of 933 base pairs. The deduced amino acid sequence of the DhlA dechlorinase exhibited 100％ homology with the corresponding enzyme from X. autotrophicus GJ10, but only 27 to 29％ homology with the corresponding enzymes from Rhodococcus rhodochrous, Pseudomonas pavonaceae, and Mycobacterium sp. strain GP1, which all dechlorinate haloalkane compounds. The UE15 strain has an ORF1 (1,356 bp) downstream from the dhlA gene. The OFR1 shows 99％ amino acid sequence homology with the transposase reported from X. autotrophicus GJ10. The transposase gene was not found in the vicinity of the dhlA in the GJ10 strain, but rather beside the dhlB gene coding for haloacid dechlorinase. The dhlA and dhlB genes were confirmed to be located at separate chromosomal loci in the Xanthobacter flavus UE15 strain as well as in X. autotrophicus GJ10. The dhlA and transposase the UE15 strain were found to be parenthesized by a pair of insertion sequences, 181247, which were also found on both sides of the transposase gene in the GJ10 strain. This unique structure of the dhlA gene organization in X. flavus strain UE15 suggested that the dechlorinase gene, dhlA, is transferred with the help of the transposase gene.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.5
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• pp.768-774
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• 2007

To study the effect of dietary docosahexaenoic acid (DHA) enrichment on the expression of hepatic genes in pigs, weaned, crossbred pigs (30 d old) were fed diets supplemented with either 2% tallow or DHA oil for 18 d. Hepatic mRNA was extracted. Suppression subtractive hybridization was used to explore the hepatic genes that were specifically regulated by dietary DHA enrichment. After subtraction, we observed 288 cDNA fragments differentially expressed in livers from pigs fed either 2% DHA oil or 2% tallow for 18 d. After differential screening, 7 genes were found to be differentially expressed. Serum amyloid A protein 2 (SAA2) was further investigated because of its role in lipid metabolism. Northern analysis indicated that hepatic SAA2 was upregulated by dietary DHA enrichment (p<0.05). In a second experiment, feeding 10% DHA oil for 2d significantly increased the expression of SAA2 (compared to the 10% tallow group; p<0.05). The porcine SAA2 full length cDNA sequence was cloned and the sequence was compared to the human and mouse sequences. The homology of the SAA2 amino acid sequence between pig and human was 73% and between pig and mouse was 62%. There was a considerable difference in SAA2 sequences among these species. Of particular note was a deletion of 8 amino acids, in the pig compared to the human. This fragment is a specific characteristic for the SAA subtype that involved in acute inflammation reaction. Similar to human and mouse, porcine SAA2 was highly expressed in the liver of pigs. It was not detectable in the skeletal muscle, heart muscle, spleen, kidney, lung, and adipose tissue. These data suggest that SAA2 may be involved in mediation of the function of dietary DHA in the liver of the pig, however, the mechanism is not yet clear.