BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes

<p>Abstract</p> <p>Background</p> <p>Overlapping genes (OGs) in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been identified. Indeed, these might prove a consistent feature across all microbial genomes. Our previous work suggests that OGs can be considered as robust markers at the whole genome level for the construction of phylogenies. An online, interactive web server for inferring phylogenies is needed for biologists to analyze phylogenetic relationships among a set of bacterial genomes of interest.</p> <p>Description</p> <p>BPhyOG is an online interactive server for reconstructing the phylogenies of completely sequenced bacterial genomes on the basis of their shared overlapping genes. It provides two tree-reconstruction methods: Neighbor Joining (NJ) and Unweighted Pair-Group Method using Arithmetic averages (UPGMA). Users can apply the desired method to generate phylogenetic trees, which are based on an evolutionary distance matrix for the selected genomes. The distance between two genomes is defined by the normalized number of their shared OG pairs. BPhyOG also allows users to browse the OGs that were used to infer the phylogenetic relationships. It provides detailed annotation for each OG pair and the features of the component genes through hyperlinks. Users can also retrieve each of the homologous OG pairs that have been determined among 177 genomes. It is a useful tool for analyzing the tree of life and overlapping genes from a genomic standpoint.</p> <p>Conclusion</p> <p>BPhyOG is a useful interactive web server for genome-wide inference of any potential evolutionary relationship among the genomes selected by users. It currently includes 177 completely sequenced bacterial genomes containing 79,855 OG pairs, the annotation and homologous OG pairs of which are integrated comprehensively. The reliability of phylogenies complemented by annotations make BPhyOG a powerful web server for genomic and genetic studies. It is freely available at <url>http://cmb.bnu.edu.cn/BPhyOG</url>.</p

Isolation, Purification, Identification and Quantum Chemical Characterization of Blood Glucose-Regulating Peptides Derived from Dry-Cured Ham of Wanzhe Spotted Pigs

To investigate the inhibitory mechanism of small peptides on carbohydrate digestion, α-amylase and α-glucosidase inhibitory fractions from the water extract and the gastropancreatic digest of dry-cured ham muscle of Wanzhe spotted pigs were separated, purified, identified, and screened for peptide sequences. And the quantum chemical calculation was used to calculate structural and charge parameters including the distribution and energy of the frontier orbitals, electrostatic charge distribution and bond length, in order to speculate the active sites. It was found that the particle size of ham muscle decreased and its hypoglycemic activity increased after proteolysis. Two (S-I and S-II) and three fractions (WY-I, WY-II and WY-III) were obtained from the water extract and the digest after Sephadex column chromatography, respectively. Using mass spectrometry, 104 peptide sequences consisting of 8–24 amino acids were identified from fraction WY-II and five sequences with Peptide Ranker scores greater than 0.7 were selected. The highest occupied orbitals of the five sequences were mainly distributed in the guanidine groups of arginine and the groups close to the amino-terminal end, while the lowest unoccupied orbitals were in the carboxyl terminals and nearby groups. Sequences with lower ΔEL-H values, GPMGPSGPR, LGFGGPSGPNAGR and APAPAPAPAPPK, might be more active. According to Coulomb’s law, the active sites of these three peptides were located at –C106H108 of arginine, –C10H12 of leucine and –C176H177 of lysine, respectively. This study could provide theoretical support for understanding the blood glucose-regulating mechanism of peptides and the nutritional value of local pig breeds

Evolutionary Dynamics of Overlapped Genes in <i>Salmonella</i>

<div><p>Presence of overlapping genes (OGs) is a common phenomenon in bacterial genomes. Most frequently, overlapping genes share coding regions with as few as one nucleotide to as many as thousands of nucleotides. Overlapping genes are often co-regulated, transcriptionally and translationally. Overlapping genes are also subject to the whims of evolution, as the gene overlap is known to be disrupted in some species/strains and participating genes are sometimes lost in independent lineages. Therefore, a better understanding of evolutionary patterns and rates of the disruption of overlapping genes is an important component of genome structure and evolution of gene function. In this study, we investigate the fate of ancestrally overlapping genes in complete genomes from 15 contemporary strains of <i>Salmonella</i> species. We find that the fates of overlapping genes inside and outside operons are distinctly different. A larger fraction of overlapping genes inside operons conserves their overlap as compared to gene pairs outside of the operons (average 0.89 vs. 0.83 per genome). However, when overlapping genes in the operons separate, one partner is lost more frequently than in those separated genes outside of operons (average 0.02 vs. 0.01 per genome). We also investigate the fate of a pan set of overlapping genes at the present and ancestral nodes over a phylogenetic tree based on genome sequence data, respectively. We propose that co-regulation plays important roles on the fates of genes. Furthermore, a vast majority of disruptions occurred prior to the common ancestor of all 15 <i>Salmonella</i> strains, which enables us to obtain an estimate of disruptions between <i>Salmonella</i> and <i>E. coli</i>.</p></div

Phylogenetic map of the overlapping gene pairs.

<p>(A) Phylogenetic map of the overlapping gene pair (<i>bcsC</i>, <i>bcsZ</i>). (B) Phylogenetic map of the overlapping gene pair (<i>ompR</i>, <i>envZ</i>).</p

Fate of the genes in pan-Overlaps in <i>Salmonella</i> strains.

<p>(A) Average of the percentages of the genes inside operons. (B) Average of the percentages of the genes outside of operons.</p

The ML phylogeny inferred from the four-fold degenerate sites of 474 genes.

<p>The internal nodes are labeled 19–35, with node 35 being the divergent point between <i>E. coli</i> and <i>Salmonella</i> and node 32 being the root node of the ingroup <i>Salmonella</i>.</p

Completely sequenced genomes analyzed in this study.

*<p>Genomes with pre-identified orthlogous clusters in ATGC <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081016#pone.0081016-Novichkov1" target="_blank">[10]</a>.</p

The Study on The Solution Structure of Full Length Primase From Bacillus subtilis

In bacterial DNA replication, DnaG primase synthesizes RNA primers which are then extended by DNA polymerase. The DnaG primase consists of three domains, N-terminal zinc-binding domain (ZBD), RNA polymerase domain (RPD) and C-terminal helicase binding domain (HBD). In the process of producing primers, the three domains of primase cooperate with each other, and none is dispensable. Although the structures of the primase domains have been reported, so far, the full-length structure of the primase is not known yet. Here, the model of full-length DnaG in Bacillus subtilis (BsuDnaG) was constructed from the data of X-ray small angle scattering (SAXS) analysis. The BsuDnaG is in extended state in solution. On the other hand, the ZBD and HBD domains could exhibit continuous conformational changes relative to the RPD domain. This study suggests the domains rearrangement in DnaG primase may facilitate its function in DNA replication

The Study on The Solution Structure of Full Length Primase From Bacillus subtilis

In bacterial DNA replication, DnaG primase synthesizes RNA primers which are then extended by DNA polymerase. The DnaG primase consists of three domains, N-terminal zinc-binding domain (ZBD), RNA polymerase domain (RPD) and C-terminal helicase binding domain (HBD). In the process of producing primers, the three domains of primase cooperate with each other, and none is dispensable. Although the structures of the primase domains have been reported, so far, the full-length structure of the primase is not known yet. Here, the model of full-length DnaG in Bacillus subtilis (BsuDnaG) was constructed from the data of X-ray small angle scattering (SAXS) analysis. The BsuDnaG is in extended state in solution. On the other hand, the ZBD and HBD domains could exhibit continuous conformational changes relative to the RPD domain. This study suggests the domains rearrangement in DnaG primase may facilitate its function in DNA replication

Export of Extracellular Polysaccharides Modulates Adherence of the Cyanobacterium <i>Synechocystis</i>

<div><p>The field of cyanobacterial biofuel production is advancing rapidly, yet we know little of the basic biology of these organisms outside of their photosynthetic pathways. We aimed to gain a greater understanding of how the cyanobacterium <i>Synechocystis</i> PCC 6803 (<i>Synechocystis</i>, hereafter) modulates its cell surface. Such understanding will allow for the creation of mutants that autoflocculate in a regulated way, thus avoiding energy intensive centrifugation in the creation of biofuels. We constructed mutant strains lacking genes predicted to function in carbohydrate transport or synthesis. Strains with gene deletions of <i>slr0977</i> (predicted to encode a permease component of an ABC transporter), <i>slr0982</i> (predicted to encode an ATP binding component of an ABC transporter) and <i>slr1610</i> (predicted to encode a methyltransferase) demonstrated flocculent phenotypes and increased adherence to glass. Upon bioinformatic inspection, the gene products of <i>slr0977, slr0982,</i> and <i>slr1610</i> appear to function in O-antigen (OAg) transport and synthesis. However, the analysis provided here demonstrated no differences between OAg purified from wild-type and mutants. However, exopolysaccharides (EPS) purified from mutants were altered in composition when compared to wild-type. Our data suggest that there are multiple means to modulate the cell surface of <i>Synechocystis</i> by disrupting different combinations of ABC transporters and/or glycosyl transferases. Further understanding of these mechanisms may allow for the development of industrially and ecologically useful strains of cyanobacteria. Additionally, these data imply that many cyanobacterial gene products may possess as-yet undiscovered functions, and are meritorious of further study.</p></div