Journal of Microbiology

Research Support, Non-U.S. Gov't

NOTE] Effects of PCR Cycle Number and DNA Polymerase Type on the 16S rRNA Gene Pyrosequencing Analysis of Bacterial Communities: Jae-Hyung Ahn , Byung-Yong Kim , Jaekyeong Song , Hang-Yeon Weon; J. Microbiol. 2012;50(6):1071-1074. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2642-z

Abstract: The effects of PCR cycle number and DNA polymerase type on 16S rRNA gene pyrosequencing analysis were investigated using an artificially prepared bacterial community (mock community). The bacterial richness was overestimated at increased PCR cycle number mostly due to the occurence of chimeric sequences, and this was more serious with a DNA polymerase having proofreading activity than with Taq DNA polymerase. These results suggest that PCR cycle number must be kept as low as possible for accurate estimation of bacterial richness and that particular care must be taken when a DNA polymerase having proofreading activity is used.

Retracted Publication

Transcriptional Analysis of the DNA Polymerase Gene of Bombyx mori Parvo-like Virus (China Isolate): Yong-Jie Wang , Ke-Ping Chen , Qin Yao , Xu Han; J. Microbiol. 2007;45(2):139-145.; DOI: https://doi.org/2521 [pii]

Abstract: The Bombyx mori parvo-like virus (China isolate) DNA polymerase (BmDNV-3 dnapol) gene has been tentatively identified based on the presence of conserved motifs. In the present study, we perform a transcriptional analysis of the BmDNV-3 dnapol gene using the total RNA isolated from BmDNV-3 infected silkworm at different times. Northern blot analysis with a BmDNV-3 dnapol-specific riboprobe showed a major transcript of 3.3 kb. 5′-RACE revealed that the major transcription start point was located 20 nucleotides downstream of the TATA box. In a temporal expression analysis using differential RT-PCR, BmDNV-3 dnapol transcript was detected at low levels at 6 h.p.i., increased from 6 to 36 h.p.i., and remained fairly constant thereafter. Analysis of the predicted DNA polymerase sequence using neighborjoining and protein parsimony algorithms indicated that the predicted 1115-residue polypeptide contained five motifs associated with DNA polymerases synthetic activities and three additional motifs associated with polymerases possessing 3′ to 5′ exonuclease activity. The molecular phylogenetic analysis of this gene supported the placement of Bombyx mori parvo-like virus in a separate virus family.

Research Support, Non-U.S. Gov't

Removal of Contaminating TEM-la β-Lactamase Gene from Removal of Contaminating TEM-la β-Lactamase Gene from: Jae Seok Song , Jung Hun Lee , Jung-Hyun Lee , Byeong Chul Jeong , Won-Keun Lee , Sang Hee Lee; J. Microbiol. 2006;44(1):126-128.; DOI: https://doi.org/2326 [pii]

Abstract: This study confirms that Taq DNA polymerase could be contaminated with the blaTEM-1a gene. It also proposes two different methods that could be used to overcome DNA contamination: (i) DNase I treatment prior to PCR amplification; and (ii) the use of a highly purified Taq DNA polymerase which was devoid of detectable contamination.

The Genetic Organization of the Linear Mitochondrial Plasmid mlp1 from Pleurotus ostreatus NFFA2: Kim, Eun Kyung , Youn, Hye Sook , Koo, Yong Bom , Roem Jung Hye; J. Microbiol. 1997;35(4):264-270.

Abstract: The structure of plasmid mlp1, a linear 10.2kb mitochondrial plasmid of Pleurotus ostreatus NFF A2 was determined by restriction enzyme mapping and partial sequencing. The plasmid encodes at least two proteins; a putative RNA polymerase showing homology to yeast mitochondrial RNA polymerase and to viral-encoded RNA polymerases, and a putative DNA polymerase showing significant homology to the family B thpe DNA polymerases. It also contains terminal inverted repeat sequences at both ends which are longer than 274 bp. A 1.6 kb EcoRI restriction fragment of m1p1 containing the putative RNA polymerase gene did not hybridize to the nuclear or motochondrial genomes from P. ostreatus, suggesting that it may encode plasmidspecific RNA polymerase. The gene fragment also did not hybridize with the RNA polymerase gene (RPO41) from Saccaromyces cerevisiae. The relationship between genes in m1p1 and those in another linear plasmid pC1K1 of Claviceps purpurea was examined by DNA hybridization. The result indicates that the genes for DNA and RNA polymerases are not closely related with those in C. purpurea.

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