• Microbiology and Biotechnology Letters
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• v.18 no.6
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• pp.640-646
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• 1990

We have cloned the cdd gene from E. coli C600 using (cdd-) as a host. From the sequenced promoter region of E=, coli cdd gene which has been determined by Valentin-Hansen P. (1985), we synthesized the 23 mer oligonucleotides corresponding to the transcription initiation region and used as a probe for cloning of the cdd gene by Southern blotting. The isolated fragments in the blotting were introduced to the colony hybridization after transforming it into the E. coli JF611 (cdd-, pyr double mutant), and we identified the hybridized band at 27 kb long. From the original insert of 27 kb fragment in theBamHI site of pBR322, the 5.3 kb fragment containing the cdd gene was isolated by subsequent deletion and subeloning. From the derived plasmid pTK509, further deletion and subcloning were performed and clarified that the cdd gene was located in the 2.1 kb of SaZI/DraI segment in the insert of pTK605. The polypeptide encoded by the cloned DNA was appeared to be a molecular mass of 33,000.

• Korean Journal of Environmental Biology
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• v.21 no.1
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• pp.56-59
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• 2003

The Salmonella typhimurium cdd gene encoding cytidine deaminase (cyti-dine/2'-deoxycytidine aminohydrolase; EC 3.5.4.5.) was isolated through shotgun clon-ing by complementation of the E. coli odd mutation. By subsequent deletion and sub-cloning from the original 3.7 Kb of EcoRI insert (pSAMI), the precise region of the cdd structural gene is located around the BglII site in the middle part of 1.7 Kb of NruI/PvuI segment. The 1.7 Kb containing odd gene wag subcloned to the pUC18 vector and the nucleotide sequence of the cdd gene was determined. When the putative ribosorne-binding site (Shine-Dalgarno sequence) and initiation codon were predicted to be GAGG at the position 459 and ATG at the position 470, respectively, there was an open reading frame of 885 nucleotides, encoding an 294 amino acid protein. The cdd gene expression in E. coli JF611/pSAMI was amplified about 50 fold compared to that of the wild type. The cdd gene expression was maintained in the stationary phase after rea-ching the peak in the late logarithmic phase.

• Journal of Microbiology and Biotechnology
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• v.1 no.1
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• pp.22-30
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• 1991

In order to secrete the Bacillus subtilis cytidine deaminase (CDase, cytidine/2'-deoxycytidine deaminase) encoded by the B. subtilis cdd gene in E. coli by the aid of signal sequences, the cdd gene was fused in-frame to either amyE or penP signal sequences and the gene expression and CDase localization were examined. For the penP signal sequence::cdd fusion, the cdd gene with 9 amino acids truncated from the 5'-terminus was fused in-frame to the signal sequence, then the $cdd^{+}$ colonies were not occurred from the minimal plate by cdd complementation. The result suggests that 9 amino acids on the $NH_2-terminal$ of CDase have an essential function in the enzyme activity. The hybrid protein obtained by fused gene amyE signal sequence::cdd structural gene gave $cdd^{+}$ phenotype and about half of the total CDase activity was found to be secreted in the periplasm of E. coli transformant JF611/pSO202. The periplasmic CDase activity of JF611 harboring pSO52 containing the intact cdd gene was considerablely lower than that of the cells harboring pSO202 carrying the hybrid cdd gene. This suggests that the CDase was secreted to the periplasm through the cytoplasmic membrane by the aid of the amyE signal sequence in the E. coli transformant.

• Microbiology and Biotechnology Letters
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• v.17 no.4
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• pp.334-342
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• 1989

The Bacillus stearothermophilus cdd gene encoding cytidine deaminase (cytidine/2'-deoxycytidine aminohydrolase; EC 3.5.4.5) was isolated through shot gun cloning by oomplementation of an E. coli cdd mutation. Primarily 3.0 kbp of the exogenote was cloned into the Pstl site of pBR322 (pJSC101). By subsequent deletion and subcloning from the insert of pJSC101 with cdd$^+$ and tetracycline resistancy, about 1.35 kbp of the EcoRI$_1$/PstI$_2$ fragment containing the cdd gene was isolated as pJSC201. The minicell experiment revealed a molecular mass of 33,000 dalton for polypeptide from the cloned DNA fragment complementing the cdd gene. From the lacZ fusion of 550 bp fragment of the EcoRI$_1$/AuaI as a putative promoter region, the transcription direction of the cdd gene on pJSC201 is from EcoRI towards the PstI sites, When the cdd gene was expressed in B. subtilis ED4O (cdd$^-$, pyr$^-$) by transformation with the E. coli-B. subtilis shuttle vector, the gene expression occured more efficiently than in E. coli and the gene appears to be stably maintained in B. subtitis as well as in E. coli.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 1986.12a
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• pp.512.2-512
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• 1986

A mutant of bacillus subtilis with a defective cdd gene encoding deoxycytidine-cytidine deaminase(EC 3.5.4.5.) has been characterized genetically. The genetic lesion causing the altered deoxycytidine-cytidine deaminase, cdd, was mapped at 225 min on the linkage map of B.subtilis by AR9 transduction Transductional analysis of the cdd region established the gene order as trp-lys-dnaE-cdd-aroD. The cdd gene was linked 72% with the aroD and 20% with the lys.

• Microbiology and Biotechnology Letters
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• v.16 no.6
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• pp.536-539
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• 1988

A mutant of Bacillus subtilis with a defective cdd gene encoding deoxycytidine-cytidine deaminase (EC 3.5.4.5) has been characterized genetically. The genetic lesion, cdd, causing the altered deoxycytidine-cytidine deaminase was mapped at 225 min on the linkage map of B. subtilis by AR9 transduction, Transductional analysis of the cdd region established the gene order in clockwise as trp-lys-cdd-aroD. The cdd gene was linked 72% with the aroD and 20% with the lys.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 1986.12a
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• pp.512.1-512
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• 1986

The cdd gene of Bacillus subtilis, encoding the deoxycytidinecytidine deaminase of pyrimidine nucleotide biosynthesis has been cloned into the EcoRl site of pBR322. The recombinant plasmid, pSol, promoted the synthesis of 100-140 fold elevated levels of the enzyme. A comparison of the polypeptides encoded by cdd complementing and non-complementing plasmids in the mini cell showed the gene product to have a molecular mass of approximately 14 kDa. The nucleotide sequence of the gene and 460 base pairs upstream from the coding region was determined. An open-reading frame, encoding a protein with a calculated molecular mass of 14337 Da, was deduced to be the coding region for cdd. However, the enzyme has an apparent molecular mass of 54 kDa as determined by gel filteration, whereas sucrose density gradient centrifugation shows 58 kDa. It means that the enzyme could be forming a tetramer in a physiological state. About 28 amino acids of the N-tetramer in a physiological state. About 28 amino acids of the N-terminal presumably form a signal for membrane translocation and six cystein residues are contained in the structure. S1 nuclease mapping indicated that transcription of cdd is initiated 17 base pairs upstream from the translational start. The structural characterization of the odd gene was performed.

• Microbiology and Biotechnology Letters
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• v.16 no.6
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• pp.468-475
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• 1988

The cloned B. subtilis cdd gene encoding cytidine/2'deoxycytidine deaminase (EC 3.5.4.5) was expressed in the cdd deficient B. subtilis mutant ED40. The gene was isolted from the cdd complementing plasmid pSO21, and inserted into the EcoR1/Pvu1 sites of pGB215-110 ΔB, which is a temperature sensitivie E. coli-B. subtilis shuttle vector. In the transformed B. subtilis ED4O harboring the resulting plasmid pSO100, cdd was expressed at several hundred fold elevated levels, and the cytidine deaminase activity in E. coli containing pSO100 was twice the level in B. subtilis/pSO0100. The Km value for cytidine of the partially purified enzyme is 1.88$\times$10$^{-4}$M at pH 7.0 and the V$_{max}$ = 11.1 $\mu$mol/min/mg of protein. The enzyme was completely inhibited by 0.1M mercaptoethanol and HgCl$_2$. The inhibition by p-chrolomercurybenzoic acid showed a Ki = 5 uM. These results suggest that sulfhydryl reagents block an active site thiol group, and/or disturb the formation of the tetrameic holoenzyme.

• Journal of Microbiology and Biotechnology
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• v.5 no.3
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• pp.125-131
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• 1995

A 3, 346 bp of the cdd upstream region in Bacillus subtilis was sequenced from the pSO1 (Song BH and J Neuhard. 1989. Mol. Gen. Genet 216: 462-468) and sequence homology was searched to the known genes in Genbank and European Molecular Biology Laboratory databanks. Five complete and one truncated putative coding sequences deduced from the nucleotide sequence were found through the ORF searching by Genetyx and Macvector software, and one of them was identified as the dgk (diacylglycerol kinase) gene and another, a truncated one, as the phoH (phosphate starvation-inducible gene) gene. The B. subtilis dgk gene, having a role for response to several environmental stress signals, revealed an open reading frame of 134 amino acids with 43.1% of sequence identity to the Streptococcus mutans dgk gene. The carboxy terminal 59 residues of the truncated phoH gene showed 52.7% and 34.5% of sequence identity in amino acids with the corresponding genes of Mycobacterium leprae and Escherichia coli. The four remaining coding sequences consisting of 115, 421, 91, and 91 residues were thought to be unknown ORFs because they have no significant similarity to known genes.

• Journal of Institute of Control, Robotics and Systems
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• v.12 no.10
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• pp.1044-1049
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• 2006

Multiple sequence alignment is a method to compare two or more DNA or protein sequences. Most of multiple sequence alignment tools rely on pairwise alignment and Smith-Waterman algorithm to generate an alignment hierarchy. Therefore, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST and CDD (Conserved Domain Database)search were combined with a clustering tool. Our clustering and annotating tool consists of constructing suffix tree, overlapping common subsequences, clustering gene sequences and annotating gene clusters by BLAST and CDD search. The system was successfully evaluated with 36 gene sequences in the pentose phosphate pathway, clustering 10 clusters, finding out representative common subsequences, and finally identifying functional domains by searching CDD database.