• Title/Summary/Keyword: Consensus sequence

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Transposition of IntAs into the Conserved Regions of IS3 Family Elements

  • Han, Chang-Gyun
    • Journal of Microbiology
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    • v.42 no.1
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    • pp.56-59
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    • 2004
  • Together with the previous reports, my computer survey revealed that several bacteria contain six copies of the type group II intron IntA. The sequence analysis of IntAs showed the high level of homology in the nucleotide sequence (91.9-99.8%). The consensus sequence, 2,270 base pair long, was derived from the nucleotide sequences of all IntA members. The size of the open reading frame intA was 502 amino acids long, that is homologous to reverse transcriptase-like proteins encoded within the group II introns. It was reported that EPEC.IntA and Sf.IntA were inserted into IS911 and IS629, respectively. The sequence of the flanking region IntA was analyzed here. The data show the insertion of EC.IntA into IS629, the insertion of EHEC.IntA into IS3, the insertion of Yp.IntA into IS904-like sequence, and the insertion of EK12.IntA into IS911. Interestingly, these IS elements nested by IntAs were the members of IS3 family elements. The sequences of the IS3 members correspond to the OrfB with the DDE motif conserved in retroviral integrases. Alignment of the flanking sequences of IntAs revealed that the flanking regions -25 to + 10 of insertion sites, that are generally believed to be required for the retrohoming, were not strongly conserved. The data presented here suggests that the retrohoming pathway of IntA seems to differ from those of other group II introns.

Random Sequence Analysis of the Genomic DNA of Methanopyrus kandleri and Molecular Cloning of the Gene Encoding a Homologue of the Catalytic Subunit of Carbon Monoxide Dehydrogenase

  • Shin, Hyun-Seock;Ryu, Jae-Ryeon;Han, Ye-Sun;Choi, Yong-Jin;Yu, Yeon-Gyu
    • 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.

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Cloning of a Laccase Gene Fragment from Ganoderma lucidum (영지버섯 Laccase 유전자의 구리결합부위 I과 IV사이 지역의 클로닝)

  • 조지현;최형태;김경훈
    • Korean Journal of Microbiology
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    • v.36 no.3
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    • pp.192-195
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    • 2000
  • Degenerate primevs corresponding to the consensus sequences of the copper-binding regions in the N- and Cterminal domains of fungal laccases were used to isolate laccase gene-specific sequences froin a white rot rungus Ganodern~a lucidrm w-hich has been known to strengthen the imnnne system. A 1.6 Kbp fragment was amplified by PCR and its base sequence was detenuiued. Locating seven iutrous within the base sequence, we could deduce its amino acid sequence. The nucleotide sequence witl~out introlls was 47Y0 identical to that of lee1 gene of Pametes wllosa; lhe identity in amino acid sequences of the two was 7994 The deduced amino acid seqoence was also sunilar to those of Coriolus versicolo~ kc3 (79%); Co~,iolz~s hirsutus phenolouiduse (78%), Trainetes vel.srcoloi. lccl (77%), Trametes ~!i/Iosa Ice2 (77%) and Trametes vemicolor kc4 (66%).

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DNA Light-strand Preferential Recognition of Human Mitochondria Transcription Termination Factor mTERF

  • Nam, Sang-Chul;Kang, Chang-Won
    • BMB Reports
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    • v.38 no.6
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    • pp.690-694
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    • 2005
  • Transcription termination of the human mitochondrial genome requires specific binding to termination factor mTERF. In this study, mTERF was produced in E. coli and purified by two-step chromatography. mTERF-binding DNA sequences were isolated from a pool of randomized sequences by the repeated selection of bound sequences by gel-mobility shift assay and polymerase chain reaction. Sequencing and comparison of the 23 isolated clones revealed a 16-bp consensus sequence of 5'-GTG$\b{TGGC}$AGANCCNGG-3' in the light-strand (underlined residues were absolutely conserved), which nicely matched the genomic 13-bp terminator sequence 5'-$\b{TGGC}$AGAGCCCGG-3'. Moreover, mTERF binding assays of heteroduplex and single-stranded DNAs showed mTERF recognized the light strand in preference to the heavy strand. The preferential binding of mTERF with the light-strand may explain its distinct orientation-dependent termination activity.

Production and Characterization of Monoclonal Antibodies to Yeast Mitochondrial RNA Polymerase Specificity Factor

  • Lee, Chang-Hwan;Jang, Sei-Heon
    • BMB Reports
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    • v.31 no.6
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    • pp.607-610
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    • 1998
  • Transcription of mitochondrial DNA in the yeast S. cerevisiae depends on recognition of a consensus nonanucleotide promoter sequence by mitochondrial RNA polymerase specificity factor, which is a 43 kDa polypeptide encoded by the nuclear MTF1 gene. Mtf1p has only limited amino acid sequence homology to bacterial sigma factors, but functions in many ways like sigma in that it is required for promoter recognition and initiation of transcription. To analyze the corebinding region of Mtf1p, monoclonal antibodies to this protein were prepared. Recombinant Mtf1p overproduced in E. coli was purified to near homogeneity and used to raise monoclonal antibodies (mAbs). From fused cells screened for Mtf1p mAbs by immunodot blot analysis, 19 positive clones were initially isolated. Further analysis of positive clones by Western blotting resulted in 4 mAbs of Mtf1p.

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Characterization of a Chalcosyltransferase (gerGTII) in Dihydrochalcomycin Biosynthesis

  • Pageni, Binod Babu;Oh, Tae-Jin;Thuy, Ta Thi Thu;Sohng, Jae Kyung
    • Molecules and Cells
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    • v.26 no.3
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    • pp.278-284
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    • 2008
  • An open reading frame, designated GerGTII and located downstream of the polyketide synthase genes, has been identified as a chalcosyltransferase by sequence analysis in the dihydrochalcomycin biosynthetic gene cluster of Streptomyces sp. KCTC 0041BP. The deduced product of gerGTII is similar to several glycosyltransferases, authentic and putative, and it displays a consensus sequence motif that appears to be characteristic of a sub-group of these enzymes. Specific disruption of gerGTII within the S. sp. KCTC 0041BP genome by insertional in-frame deletion method, resulted complete abolishment of dihydrochalcomycin and got the 20-O-mycinosyl-dihydrochalconolide as intermediate product in dihydrochalcomycin biosynthesis which was confirmed by electron spray ionization-mass spectrometry and liquid chromatography-mass spectrometry. Dihydrochalcomycin also was recovered after complementation of gerGTII.

Selection of Putative Iron-responsive Elements by Iron Regulatory Protein-2

  • Kim, Hae-Yeong
    • Journal of Applied Biological Chemistry
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    • v.42 no.2
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    • pp.62-65
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    • 1999
  • Iron regulatory proteins (IRPs) 1 and 2 bind with equally high affinity to specific RNA stem-loop sequences known as iron-responsive elements (IRE) which mediate the post-transcriptional regulation of many genes of iron metabolism. To study putative IRE-like sequences in RNA transcripts using the IRP-IRE interaction, Eight known genes from database were selected and the RNA binding activity of IRE-like sequences were compared to IRP-2. Among them, the IRE-like sequence in 3'-untranslational region (UTR) of divalent ration transporter-1 (DCT-1) shows a significant RNA binding affinity. This finding predicts that IRE consensus sequence present within 3'-UTR of DCT-1 might confer the regulation by IRP-2.

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Chitosan surface grafted with fusion protein of FGF-2 and Fibronectin-FGF for tissue regeneration therapy

  • Hwang, Jeong-Hyo;Lee, Jue-Yeon;Kim, Sun-Chul;Jang, Jun-Hyeog;Ku , Young;Chung, Chong-Pyoung;Lee, Seung-Jin
    • Proceedings of the PSK Conference
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    • 2003.10b
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    • pp.231.3-232
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    • 2003
  • The biomedical applications of chitosan have been widely researched. FN mediates its biological effects through binding to the hetero-dimeric transmembrane glycoproteins, integrins, which physically couple the cytoskeleton to the ECM. FN binds to the integrin through a consensus site including the Arg-Gly-Asp (RGD) sequence within tenth type III module (Ruoslahti & Pierschbacher 1987). A short sequence Pro-His-Ser-Arg-Asn (PHSRN) has also been identified as a synergistic motif within ninth type III module for binding to ${\alpha}$5${\beta}$1 integrin (Aota et al. 1994). (omitted)

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Direct Interaction Between Akt1 and Gcn5 and its Plausible Function on Hox Gene Expression in Mouse Embryonic Fibroblast Cells

  • Oh, Ji Hoon;Lee, Youra;Kong, Kyoung-Ah;Kim, Myoung Hee
    • Biomedical Science Letters
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    • v.19 no.3
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    • pp.266-269
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    • 2013
  • Hox genes encode transcription factors important for anterior-posterior body patterning at early stages of embryonic development. However, the precise mechanisms by which signal pathways are stimulated to regulate Hox gene expression are not clear. In the previous study, protein kinase B alpha (Akt1) has been identified as a putative upstream regulator of Hox genes, and Akt1 has shown to regulate Gcn5, a prototypical histone acetyltransferase (HAT), in a negative way in mouse embryonic fibroblast (MEF) cells. Since the activity of HAT such as the CBP/p300, and PCAF (a Gcn5 homolog), was down-regulated by Akt through a phosphorylation at the Akt consensus substrate motif (RXRXXS/T), the amino acid sequence of Gcn5 protein was analyzed. Mouse Gcn5 contains an Akt consensus substrate motif as RQRSQS sequence while human Gcn5 does not have it. In order to see whether Akt1 directly binds to Gcn5, immunoprecipitation with anti-Akt1 antibody was carried out in wild-type (WT) mouse embryonic fibroblast (MEF) cells, and then western blot analysis was performed with anti-Akt1 and anti-Gcn5 antibodies. Gcn5 protein was detected in the Akt1 immunoprecipitated samples of MEFs. This result demonstrates that Akt1 directly binds to Gcn5, which might have contributed the down regulation of the 5' Hoxc gene expressions in wild type MEF cells.

A Survey of the Brassica rapa Genome by BAC-End Sequence Analysis and Comparison with Arabidopsis thaliana

  • Hong, Chang Pyo;Plaha, Prikshit;Koo, Dal-Hoe;Yang, Tae-Jin;Choi, Su Ryun;Lee, Young Ki;Uhm, Taesik;Bang, Jae-Wook;Edwards, David;Bancroft, Ian;Park, Beom-Seok;Lee, Jungho;Lim, Yong Pyo
    • Molecules and Cells
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    • v.22 no.3
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    • pp.300-307
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    • 2006
  • Brassica rapa ssp. pekinensis (Chinese cabbage) is an economically important crop and a model plant for studies on polyploidization and phenotypic evolution. To gain an insight into the structure of the B. rapa genome we analyzed 12,017 BAC-end sequences for the presence of transposable elements (TEs), SSRs, centromeric satellite repeats and genes, and similarity to the closely related genome of Arabidopsis thaliana. TEs were estimated to occupy 14% of the genome, with 12.3% of the genome represented by retrotransposons. It was estimated that the B. rapa genome contains 43,000 genes, 1.6 times greater than the genome of A. thaliana. A number of centromeric satellite sequences, representing variations of a 176-bp consensus sequence, were identified. This sequence has undergone rapid evolution within the B. rapa genome and has diverged among the related species of Brassicaceae. A study of SSRs demonstrated a non-random distribution with a greater abundance within predicted intergenic regions. Our results provide an initial characterization of the genome of B. rapa and provide the basis for detailed analysis through whole-genome sequencing.