Uptake of Polycyclic Aromatic Hydrocarbons across Bacterial Membrane

Polycyclic aromatic hydrocarbons (PAHs) are important pollutants, whose biodegradation and bioremediation with microorganisms are the promising ways to clean environments and reduce their exposure to humans. Although the transportation of PAHs across bacterial membrane is the first step forwards their biodegradation, it receives less attention. In this mini-review, we explore which transport system for uptake of carbon sources can serve for uptake of PAHs in bacteria, and try to uncover some patterns in their transport mechanisms. Collectively, 1) the major carbohydrate transport system, PTS, is unlikely to take PAHs because PAHs lack a hydroxy group for phosphorylation but aromatic acids are good candidates;2) PAHs could probably go through H+ symporters, especially the low-molecular-weight PAHs, which are partially dissolvable in water;3) it is unlikely that PAHs can produce chemiosmotic ion gradients to go through uniporters;and 4) antiporters could serve as transporters to transport PAHs across bacterial membrane only after the metabolism of PAHs generates extra H+ inside cell. Accordingly, the basic mechanism for uptake of PAHs is whether they can donate H+ in order to generate an electrochemical proton gradient to go through symporters.

Elaboration of Simplest Folding Structures in 2-Dimensional Lattice with Delta-Hemolysin and Its Variants in HP Model

Although the advanced 3-dimensional structure measurements provide more and more detailed structures in Protein Data Bank, the simplest 2-dimensional lattice model still looks meaningful because 2-dimensional structures play a complementary role with respect to 3-dimensional structures. In this study, the folding structures of delta-hemolysin and its six variants were studied at 2-dimensional lattice, and their amino acid contacts in folding structures were considered according to HP model with the aid of normalized amino acid hydrophobicity index. The results showed that: 1) either delta-hemolysin or each of its variants could find any of its folding structure in one eighth of 1,129,718,145,924 folding structures because of symmetry, which reduces the time required for folding, 2) the impact of pH on folding structures is varying and associated directly with the amino acid sequence itself, 3) the changes in folding structures of variants appeared different case by case, and 4) the assigning of hydrophobicity index to each amino acid was a way to distinguish folding structures at the same native state. This study can help to understand the structure of delta-hemolysin, and such an analysis can shed lights on NP-problem listed in millennium prize because the HP folding in lattice belongs to a sub-problem of NP-problem.

Correlation of Combined Characters of Amino Acid and Whole Protein with Success Rate of Crystallization of <i>Lactobacillus</i>Proteins

Crystallization of proteins is a very delicate process, which is influenced by many known and unknown factors. Of tested factors, many factors are exclusively related to individual amino-acid characters such as molecular weight or protein characters such as protein length. It is considered necessary to test factors that combine both individual amino-acid characters and protein characters with respect to success rate of crystallization. In this study, two combined characters characterizing individual amino-acid character and protein character, amino acid distribution probability and future composition, were used to correlate the success rate of crystallization of proteins from Lactobacillus via modeling. The results obtained from logistic regression and neural network were compared against the results obtained from each of 533 individual amino-acid characters. This study demonstrated that the combined characters are involved in crystallization process and should be taken into account for predicting the success rate of crystallization process.

2-Dimensional HP Foldings of Dermaseptin-J2

Although the hydrophobic-polar (HP) model is a simple model to study protein folding, it is an approximation to the real-life case. Dermaseptin is a subfamily of frog skin active peptide family, which has various antimicrobial activities, and dermaseptin-J2 is a newly found peptide composed of 26 amino acids. In this study, the 2-dimensional HP model was used to analyze the foldings of dermaseptin-J2 and its nine mutants, which were converted to different HP sequences according to the normalized amino acid hydrophobicity index with respect to pH levels and the conversion of glycine as hydrophobic or polar, and each has 847,288,609,443 possible foldings. The results show that the foldings with minimal energy have different native states, which are chiral and can be numerically distinguished and ranked according to the normalized amino acid hydrophobicity index. The nine mutants of dermaseptin-J2 do not affect the minimal energy but affect their native states at pH 7. The results demonstrate that two pH levels and conversion of glycine as hydrophobic or polar affect the native state and minimal energy, suggesting these are two ways to modify dermaseptin-J2.

Adaptation in polymerase basic protein 1 family from influenza A virus to climate change

Global climate changes affect the functioning of ecosystems, in particular host-pathogen interactions, with major consequences in health ecology, however, it is less addressed how the change in global temperature affects the protein family of influenza virus. In this study, we studied the adaptation of polymerase basic protein 1 (PB1) family from influenza A virus to temperature change. 3841 PB1 proteins sampled from 1956-2011 were quantified by the amino-acid pair predictability and then compared their general changes with the temperature changes (Had-CRUT3v and CRUTEM4v data sets) of corresponding years on a 5? by 5? grid-box basis. Also, point-to-point comparisons were conducted from 1956 to 1998 in all and different species. The results showed that both changes in the temperature and unpredictable portion of PB1 proteins had similar trends from 1956 to 2011, which provides the evidence of virus adaptation at protein level to climate change.

Building Quantitative Gene Regulatory Mechanism in Quorum Sensing in <i>Pseudomonas aeruginosa</i>Using Transcriptomic Data

A large amount of transcriptomic data provides opportunities 1) to verify the gene regulatory mechanism, which is usually obtained from a single experiment, at population level;2) to uncover the gene regulatory mechanism at population level;and 3) to build a quantitatively gene regulatory mechanism. One of the best studied regulatory mechanisms in bacteria is the quorum sensing (QS), which plays an important role in regulation of bacteria population behaviors such as antibiotic production, biofilm formation, bioluminescence, competence, conjugation, motility and sporulation. Pseudomonas aeruginosa is a Gram-negative bacterium causing diseases in plants, animals, humans, and its biofilm and drug-resistance become great concerns in clinics. P. aeruginosa has three QS systems including a specific one for Pseudomonas. In this study, the transcriptomic data of P. aeruginosa were combined from 104 publications and QS gene expressions were analyzed under different experimental conditions. The results demonstrate the quantitatively regulatory mechanisms of QS genes at population level including 1) to rank and group QS-related genes according to their activity;2) to quantitatively define the role of a single global regulator;3) to find out the probability that a global regulator impacts QS genes and the probability that a QS gene responds to global regulators;and 4) to search for overlapped genes under four types of experimental conditions. These results provide integrative information on understanding the regulation of QS genes at population level.

Mutation Patterns in Lysostaphin

Lysostaphin is widely used in clinical settings against Staphylococcus aureus, but its mutants can abolish its killing activity. The difficulty in studies of mutations in lysostaphin is the shortage of data, which may need many decades to collect, although lysostaphin is so important for clinical therapeutics and drug development. In order not to passively wait for the accumulation of new data, in this study 1) the 23,442 mutations in 1408 proteins from databank were used to determine whether the mutations in lysostaphin follow the general mutation trend obtained from the databank, 2) the amino-acid pair predictability was used to explore the underlined mechanism for lysostaphin mutations, and 3) the amino-acid distribution probability was used to associate the mutation with dysfunction of lysostaphin. The results show that the mutations in lysostaphin follow the general trend of mutations in proteins;the underlined mechanism for mutations in lysostaphin is explainable from a viewpoint of randomness, and a mutation with increased distribution probability would have a larger chance to dysfunction lysostaphin. This study provides useful information for future design of anti-S. aureus drug and enzyme engineering.

Synthesis of Fluorescent Carbon Quantum Dots from Dried Lemon Peel for Determination of Carmine in Drinks

Carbon quantum dots（CQDs） with a quantum yield of 11% were synthesized via a simple, low-cost and green hydrothermal treatment using dried lemon peel as carbon source. The obtained CQDs showed a strong emission at the wavelength of 505 ran with an optimum excitation of 425nm. Carmine with maximum absorption wavelength at 508 nm could selectively quench the fluorescence of CQDs. Based on this principle, a fluorescence probe was developed for carmine determination. The quenching mechanism of CQDs was elucidated. A linear relationship was found in the carmine concentration range of 0.20-30.00 mg/L with the detection limit（3a/k） of 0.16 mg/L. Satisfac- tory results were achieved when the method was applied for the determination of carmine in soft drinks.

Arabidopsis thaliana NOP10 is required for gametophyte formation

The female gametophyte is crucial for sexual reproduction of higher plants, yet little is known about the molecular mechanisms underlying its development. Here, we report that Arabidopsis thaliana NOP10 （AtNOP10） is required for female gametophyte formation. AtNOP10 was expressed predominantly in the seedling and reproductive tissues, including anthers, pollen grains, and ovules. Mutations in AtNOP10 interrupted mitosis of the functional megaspore during early development and prevented polar nuclear fusion in the embryo sacs. AtNOP10 shares a high level of amino acid sequence similarity with Saccharornycescerevisiae （yeast） NOPIo （ScNOP1o）, an important compo- nent of the H/ACA small nucleolar ribonucleoprotein particles （H/ACA snoRNPs） implicated in 18S rRNA synthe- sis and rRNA pseudouridylation. Heterologous expression of ScNOP10 complemented the mutant phenotype of Atnop10. Thus, AtNOPIo influences functional megaspore mitosis and polar nuclear fusion during gametophyte formation in Arabidopsis.