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Analysis of DNA transcription termination sequences of gene coding for phaC1 polymerase in Pseudomonas species

Możejko J., Królicka M., Ciesielski S.

Environmental Biotechnology

2011

Vol. 7, No. 1

12-16

Polyhydroxyalkanoates (PHAs) are natural polyesters that are synthesized by many bacteria as an intracellular carbon and energy compound. Medium-chain-length polyhydroxyalkanoates (mcl-PHAs) have gained much interest in research on microbial biopolymers because of their ease of chemical modification. Mcl-PHAs are naturally synthesized by Pseudomonas species by transformation of wide range of substrates. The physiological background of mcl-PHAs synthesis is known, and key genes engaged in this process are discovered already, but the knowledge about their molecular regulation is still limited. Especially, there is lack of information concerning the transcription termination of gene coding for PHA polymerase (phaC1). It is assumed that the main role could play Rho-independent termination, which is related to presence of palindromic sequences, which leads to formation of the hairpin structure and to dissociation of the ternary elongation complex (TEC). In this work, DNA sequences located after phaC1 gene belonging to nineteen Pseudomonas strains were investigated. Among all analyzed strains, five had palindromic sequences, typical for Rhoindependent terminators. Our results proved, that gene phaC1, coding for PHA polymerase, can be independently regulated only in some species.

Sequence similarity based method for protein function prediction

Blazewicz J., Lukasiak P., Milostan M., Krasnogor N., Jackowiak P.

Foundations of Computing and Decision Sciences

2009

Vol. 34, No. 3

173-191

Motivation: Proteins are the main building blocks of life. They catalyze biological processes in living cells to sustain life and improve metabolism. They also act as biological scaffolds and are cell's workhorses. As a matter of fact, knowing their function is one of the most important milestones for understanding life.The function depends on the tertiary structure of the protein, but only for a fraction of amino acid sequences gathered in databases the structure is known. Thus, creation of efficient and accurate methods that predict function from sequences, based on already known function-sequence assignments, is a fundamental challenge in computational biology. Results: First, we show a detailed analysis of a usability of similarity search engines in the context of function prediction. Then we propose a simple and effective method for assigning function to sequences based on the results of similarity searches and information gathered from gene ontology annotation graphs. Availability: All data used for the analysis presented in this paper as well as raw result are available at the site: http://bio.cs.put.poznan.pl/funcpred/data/ Suplementary Material: Suplementary materials with additional charts are available at: http://bio.es.put.poznan.pl/funcpred/suplement/ Contact: protbio@cs.put.poznan.pl