Papers by Keyword: Phylogeny

Abstract: The mitochondria are organelles found within eukaryotic cell, possess own small circular DNA (mtDNA) apart from the most of DNA found in cell nucleus. The transcription and translation of mtDNA requires tRNA that often encoded by mtDNA itself. The mtDNA evolves faster than genomic DNA primary due to mitochondrial dysfunction and pathogenesis. The genes of mitochondria tRNA (mt tRNA) are prone to mutate that links to mitochondrial activity and protein synthesis machinery. It is important to understand the codon use by mt tRNA for Acheta domesticus to understand evolutionary relationship within closely related species and mitochondrial protein synthesis machinery. The present study uses the High throughput RNA sequencing data to identify mt tRNA genes using to examine the codon use for mitochondrial protein synthesis process. The conservative property of tRNA secondary structure assisted identified and confirmed anchored tRNA sequences with respective amino acid anticodon according to genetic code for tRNA in mtDNA. This study provides mt tRNA sequences to understand evolution of mitochondrial tRNA of Acheta domesticus with other related species to establish phylogeny. Moreover, mt tRNAs are the exons that provides partial sequences for mitochondria DNA. The novel approach for tRNA identification will guide other studies for PCR free in silico analysis.

Abstract: Rbcl gene of 13 Lilium species were amplified, sequenced and analyzed. By comparing the rbcL sequences with 32 other species retrieved from GenBank, the sequence divergences and the phyletic evolution were analyzed and the phylogenetic tree was constructed. All rbcL sequences across 45 species are 732 bp with an average GC content of 45.1%. Potentially parsimony informative characters (PIC) are 39. From the phylogenetic tree, it can be found that it consists of three branches which are Liliaceae Lilium (I), other Liliaceae genus (II), Trilliaceae and Palmae (III).3D model was structured by homology comparative SWISS-Model online and showed with RasTop sofeware.The evolutionary analyses from the site-specific model, the 142nd and 225th codon sites are found to be under positive selection in rbcL gene.

Abstract: A bacterial strain NAPZ, which utilized polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source for growth, was studied on its apparent characteristics, key gene structure and functions. It was preliminarily identified as a Bacillus sp. according to its physiological characteristics and the phylogenetic property of its 16S rRNA gene sequence. Based on the reported RHD gene sequences, a pair of primers was designed to amplify the RHD gene from the genomic DNA of strain NAPZ by PCR. Then, the RHD gene was cloned and sequenced. Based on this sequence and its related sequences in the GenBank database, a multiple alignment was conducted then a phylogenetic tree was constructed with DNAMAN and MEGA software. The analysis revealed that strain NAPZ oxidized PAHs via ring hydroxylating dioxygenase (RHD) pathway. The study provided experimental and theoretical support for revealing the structure and function of key genes as well as the PAHs-degrading pathways in strain NAPZ.

Abstract: A Gram-positive, strictly aerobic and moderately halophilic bacterial strain HSD was obtained from the sea water sample collected from International Sea Water Bathing Place in Weihai, a city on the shore of the Yellow Sea. Strain HSD was bacillus. The optimum growth temperature was 32~37°C and the optimum pH was 6.0~9.0. It could grow well at 100 g•L-1 salt mass concentration. The G+C mole fraction of its genomic DNA was 37.5%. 16S rRNA gene sequence indicated a close relationship to Alkalibacillus halophilus (DQ359731) with similarity of 99%. However, they had obvious difference in whole-cell main fatty acid components, cell size, cell morphology, motility, oxidase, gelatine liquefication, nitrate reduction, NaCl tolerance range, pH tolerance range, G+C mole fraction, sole carbon source, sole nitrogen source, antibiotic sensitivity and a source of the strain isolation. Comparing of these taxonomic characters of strain HSD with those of other type strains of the genus Alkalibacillus, the differences were more obvious. In view of multiple identification results, it was proposed that strain HSD was classified as the type strain of a new species of the genus Alkalibacillus under the name Alkalibacillus huanghaiensis sp.nov..

Abstract: A Gram-positive, strictly aerobic, spore-bearing and moderately halophilic bacterial strain HNPHT was obtained from the sea mud sample collected from Jinhaitan Park in Weihai, a city on the shore of the Yellow Sea. Strain HNPHT was bacillus. The optimum growth temperature was 30-36°C and the optimum pH was 6.5-9.5. It could grow well at 5-20% salt concentration. The G+C content of its genomic DNA was 37.0%. 16S rRNA gene sequence indicated a close relationship to Alkalibacillus halophilus (DQ359731) and Alkalibacillus salilacus (AY671976) with similarity of 99%. However, they had obvious difference in whole-cell main fatty acid components, cell size, cell morphology, colony color, motility, oxidase, gelatine liquification, nitrate reduction, NaCl tolerance range, pH tolerance range, G+C mole fraction, sole carbon source, sole nitrogen source, antibiotic sensitivity and a source of the strain isolation. A comparison of these taxonomic characters of strain HNPHT with those of some type strains of the genus Alkalibacillus indicated that the strain could be distinguished from A. halophilus and A. salilacus. In view of multiple identification results, it was proposed that strain HNPHT was classified as the type strain of a new species of the genus Alkalibacillus under the name Alkalibacillus weihaiensis sp. nov..

Abstract: The function of AcoX, encoded by acoX existing in aco clusters which are responsible for acetoin catabolism in some microbes from the Kingdoms of Bacteria and Archaea, remained unknown till today. Although some AcoXs were annotated as ATP-NAD kinases in bioinformatics databases, AcoXs were found to form an independent family during evolution in this study. By bioinformatic analysis and molecular comparison, AcoX was postulated to have the catalytic function of acetoin phosphorylation. The AcoX from Pseudomonas putida KT2440 was expressed in Escherichia coli using the pET28a vector. The His-tagged AcoX was purified and digested by thrombin. The deconvolution of circular dichroism spectra using K2d algorithm indicates a >28% and >14% content for alpha and beta structures in AcoX, respectively. But unfortunately, not only the activities of NAD kinase, pyruvate kinase, and methylglyoxal synthase, but also the postulated enzymatic activity of acetoin kinase was not detected under all the conditions studied.

Abstract: Arsenic resistance genes were isolated from the moderately thermophilic, Gram-positive iron and sulfur-oxidizing bacterium, Sulfobacillus thermosulfidooxidans. Only arsR and arsB genes were present and attempts to identify an arsC using degenerate PCR primers or dependent arsC genes as probes in Southern hybridization experiments were unsuccessful. Although enhanced resistance to arsenite was not detected when the ars genes were cloned in Escherichia coli, the kumamolisin-As and arsRB genes were induced by arsenite. RT-PCR experiments suggested that transcription of the cloned kumamolisin-As-like and arsRB genes is linked in Escherichia coli, but not in Sb. thermosulfidooxidans. The gene order kumamolisin-As precursor, arsR and arsB was maintained among three strains of Sb. thermosulfidooxidans isolated from three continents. Southern hybridization using a Sb. thermosulfidooxidans arsB gene fragment as a probe gave a positive hybridization signal using S. acidophilus but not with S. thermotolerans genomic DNA. Comparison of partial sequence data of the arsB and 16S rRNA genes suggested that the two types of genes have undergone a similar evolutionary history and therefore that the arsB genes were present in the ancestral Sulfobacillus before its divergence into species.

Abstract: It has long been recognized that isolates of iron- and sulfur-oxidizing acidophiles referred to as “Acidithiobacillus ferrooxidans” probably include more than one species, on the basis of differences in chromosomal GC contents and 16S rRNA gene sequences. Phylogenetic heterogeneity among these isolates was confirmed by phylogenetic analysis using the sequences of the 16S-23S intergenic spacers (ITS). Two main groups have been identified: the first includes the type strain of Acidithiobacillus ferrooxidans and a second comprises a cluster of newly isolated strains that have 98.5% 16S rRNA gene sequence identity with the type strain. Given that the new group of isolates have GC contents of 56 mol% as opposed to 58.8 mol% for At. ferrooxidansT, and that they share only 37% homologous DNA, these were given the new species name Acidithiobacillus ferrivorans. Further studies showed that, while strains of At. ferrivorans have many physiological traits in common with At. ferrooxidans, they also differ in some key characteristics. These include the ability to grow at temperatures as low as 4°C (as opposed to the lower limit of between 10 and 12°C for At. ferrooxidans) and the greater sensitivity of At. ferrivorans to low pH (minimum of 1.9 for growth as opposed to 1.3 for At. ferrooxidansT). Important genotypic differences include the fact that all strains of At. ferrivorans do not contain the archetypal rusticyanin gene (rusA), rather most contain a rusA homologue (rusB). Furthermore, the high potential iron-sulfur protein-encoding gene of all At. ferrivorans strains analyzed is more similar to the iro than to the hip gene characterized in At. ferrooxidansT. These results suggest that the iron oxidation pathways are different in At. ferrivorans and At. ferrooxidans.