Journal of Microbiology

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

Studies on Synonymous Codon and Amino Acid Usage Biases in the Broad-Host Range Bacteriophage KVP40: Keya Sau , Sanjib Kumar Gupta , Subrata Sau , Subhas Chandra Mandal , Tapash Chandra Ghosh; J. Microbiol. 2007;45(1):58-63.; DOI: https://doi.org/2490 [pii]

Abstract: In this study, the relative synonymous codon and amino acid usage biases of the broad-host range phage, KVP40, were investigated in an attempt to understand the structure and function of its proteins/proteincoding genes, as well as the role of its tRNAs. Synonymous codons in KVP40 were determined to be ATrich at the third codon positions, and their variations are dictated principally by both mutational bias and translational selection. Further analysis revealed that the RSCU of KVP40 is distinct from that of its Vibrio hosts, V. cholerae and V. parahaemolyticus. Interestingly, the expression of the putative highly expressed genes of KVP40 appear to be preferentially influenced by the abundant host tRNA species, whereas the tRNAs expressed by KVP40 may be required for the efficient synthesis of all its proteins in a diverse array of hosts. The data generated in this study also revealed that KVP40 proteins are rich in low molecular weight amino acid residues, and that these variations are influenced primarily by hydropathy, mean molecular weight, aromaticity, and cysteine content.

Biosynthesis of Poly-β-Hydrozyalkanoates by Bacillus thuringiensis R-510: Lee, Kang Tae , Kim, Jeong Yoon , Rhee, young Ha , Bae, Kyung Sook , Kim, Young Baek; J. Microbiol. 1995;33(1):59-65.

Abstract: Synthesis and accumulation of Poly-β-Hydrozyalkanoates (PHA) in Bacillus thuringiensis R-510 isolated from soil were investigatd. This organism was resistant to relatively higj concentration of propionate and had a capability of accumulatinf copolymers consisting of 3-hydroxybutyrate(3HB) and 3-hydroxyvalerate(3HV) when the medium was supplemented with propionate as a precursor, The PHA content maximally reached up to 44.5% of dry cell weight in the presence of 0.1% propionate. The molar fraction of 3HV in the copolymer was increased from 19.4 to 80,2 mol% by adding 0.05 to 0.5% propionate to glucose medium. The addition of propionate during exponential or stationary phase of cell growth was less effective for the enhancement of 3HV content in the copolymer, although cell mass and PHA content were not affected by the time of propionate addition. PHB homopolymer and copolymer produced by B. thuringiensis R-510 were measured to have number average molecular weights in the range of 53,000 to 65,000. Polydispersity indices were between 1.5 and 2.2. Some of the produced polymers had bimodal molecular weight distribution.

Culture conditions affecting the molecular weight distribution of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthesized by alcaligenaes sp. SH-69: Yoon, Joo Seok , Park, Sang Kyu , Kim, Young Baek , Maeng, Hack Young , Rhee, Young Ha; J. Microbiol. 1996;34(3):279-283.

Abstract: The weight average molecular weight of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthesized by Alcaligenes sp. SH-69 was altered between 3.2 × 10^5 and 1.1 × 10^6 depending upon various culture conditions. It appeared that culture conditions favorable for the efficient production of copolyesters promoted the formation of higher molecular weight copolyesters. Polydispersity indices of isolated copolyesters were in the range of 1.5 to 2.5.

Evaluation of Several Parameters of in situ Polymerase Chain Reaction (ISPCR) to Reduce the Leakage of Amplificants from Cells: Jae Yung Lee , Chung-Kyoon Auh , George W. Jordan; J. Microbiol. 2002;40(1):70-76.

Abstract: Proviral DNAs from HIV-1-infected CD4+ T cells (Molt/LAV cells) were amplified and detected in infected individual cells using polymerase chain reaction and in situ hybridization. In this in situ PCR, three parameters were considered to achieve effective amplification and retention of amplificants inside the cells by making high molecular weight PCR products intracellularly, forming agarose matrix against the cells, and maintaining the appropriate PCR temperature profile. Over the cycles of amplification, tailed primers with complementary overhanging sequences at their 5 sides manufactured high molecular weight products by using short primary products as a repeating unit. Agarose matrix could prevent the diffusion of the amplificants from the cells. Use of Thermanox coverslip inside the PCR tube offered target cells a similar temperature profile to that of conventional PCR in solution.

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