Cometabolic degradation mechanism and microbial network response of methanotrophic consortia to chlorinated hydrocarbon solvents.

The cometabolism mechanism of chlorinated hydrocarbon solvents (CHSs) in mixed consortia remains largely unknown. CHS biodegradation characteristics and microbial networks in methanotrophic consortia were studied for the first time. The results showed that all CHSs can efficiently be degraded via cometabolism with a maximum degradation rate of 4.8 mg/(h·gcell). Chloroalkane and chloroethylene were more easily degraded than chlorobenzenes by methanotrophic consortia, especially nonfully chlorinated aliphatic hydrocarbons, which were converted to Cl- with a production rate of 0.29-0.36 mg/(h·gcell). In addition, the microecological response results indicated that Methylocystaceae (49.0%), Methylomonas (65.3%) and Methylosarcina (41.9%) may be the major functional degraders in methanotrophic consortia. Furthermore, the results of the microbial correlation network suggested that interactive relationships constructed by type I methanotrophs and heterotrophs determined biodegradability. Additionally, PICRUSt analysis showed that CHSs could increase the relative abundance of CHS degradation genes and reduce the relative abundance of methane oxidation genes, which was in good agreement with the experimental results.

Biodegradation of phenol by a highly tolerant strain Rhodococcus ruber C1: Biochemical characterization and comparative genome analysis.

A novel phenol-degrading strain was isolated and identified as Rhodococcus ruber C1. The degradation analysis shows that 1806 mg/L of phenol can be completely degraded by strain C1 within 38 h, and the maximum specific growth rate (µmax=1.527 h-1) and maximum specific phenol degradation rate (qmax=3.674 h-1) indicate its excellent phenol metabolism capability. More importantly, phenol can be degraded by strain C1 in the temperature range of 20-45 °C within 72 h, and with longer degradation time, phenol can be completely degraded even at 10, 15 and 50 °C. The whole genome of strain C1 was sequenced, and a comparative genome analysis of strain C1 with 36 other genomes of Rhodococcus was performed. A remarkable gene family expansion occurred during the evolution of Rhodococcus, and a comprehensive evolutionary picture of Rhodococcus at genomic level was presented. Moreover, the copy number of genes involved in phenol metabolism was compared among genus Rhodococcus, and the results demonstrate high phenol degradation capability of strain C1 at genomic level. These findings suggest that Rhodococcus ruber C1 is a bacterium capable of degrading phenol efficiently in the temperature range of 10-50 °C.

[Sequence analysis of 16S rDNA and pmoCAB gene cluster of trichloroethylene-degrading methanotroph].

Methanotrophs could degrade methane and various chlorinated hydrocarbons. The analysis on methane monooxygenase gene cluster sequence would help to understand its catalytic mechanism and enhance the application in pollutants biodegradation. The methanotrophs was enriched and isolated with methane as the sole carbon source in the nitrate mineral salt medium. Then, five chlorinated hydrocarbons were selected as cometabolic substrates to study the biodegradation. The phylogenetic tree of 16S rDNA using MEGE5.05 software was constructed to identify the methanotroph strain. The pmoCAB gene cluster encoding particulate methane monooxygenase (pMMO) was amplified by semi-nested PCR in segments. ExPASy was performed to analyze theoretical molecular weight of the three pMMO subunits. As a result, a strain of methanotroph was isolated. The phylogenetic analysis indicated that the strain belongs to a species of Methylocystis, and it was named as Methylocystis sp. JTC3. The degradation rate of trichloroethylene (TCE) reached 93.79% when its initial concentration was 15.64 µmol/L after 5 days. We obtained the pmoCAB gene cluster of 3 227 bp including pmoC gene of 771 bp, pmoA gene of 759 bp, pmoB gene of 1 260 bp and two noncoding sequences in the middle by semi-nested PCR, T-A cloning and sequencing. The theoretical molecular weight of their corresponding gamma, beta and alpha subunit were 29.1 kDa, 28.6 kDa and 45.6 kDa respectively analyzed using ExPASy tool. The pmoCAB gene cluster of JTC3 was highly identical with that of Methylocystis sp. strain M analyzed by Blast, and pmoA sequences is more conservative than pmoC and pmoB. Finally, Methylocystis sp. JTC3 could degrade TCE efficiently. And the detailed analysis of pmoCAB from Methylocystis sp. JTC3 laid a solid foundation to further study its active sites features and its selectivity to chlorinated hydrocarbon.

Characterization of Methylocystis strain JTA1 isolated from aged refuse and its tolerance to chloroform.

To accelerate the efficiency of methane biodegradation in landfills, a Gram-negative, rod-shaped, non-motile, non-spore-forming bacterium, JTA1, which can utilize methane as well as acetate, was isolated from the Laogang MSW landfills, Shanghai, China. Strain JTA1 was a member of genus Methylocystis on the basis of 16S rRNA and pmoA gene sequence similarity. The maximum specific cell growth rates (micro(max) = 0.042 hr(-1), R2 = 0.995) was derived through Boltzmann simulation, and the apparent half-saturation constants (K(m(app)) = 7.08 mmol/L, R2 = 0.982) was calculated according to Michaelis-Menton hyperbolic model, indicating that Methylocystis strain JTA1 had higher-affinity potential for methane oxidation than other reported methanotrophs. By way of adding the strain JTA1 culture, the methane consumption of aged refuse reached 115 mL, almost two times of control experiment. In addition, high tolerance of Methylocystis strain JTA1 to chloroform could facilitate the methane oxidation of aged refuse bio-covers. At the chloroform concentration of 50 mg/L, the methane-oxidation rate of bio-cover reached 0.114 mL/(day x g), much higher than the highest rate, 0.0135 mL/(day x g), of reported bio-covers. In conclusion, strain JTA1 opens up a new possibility for environmental biotechnology, such as soil or landfills bioremediation and wastewater decontamination.

Predicting the activity of antimicrobial peptides with amino acid topological information.

In this paper, VSTPV, was recruited as a novel set of structural and topological descriptors derived from principal component analysis (PCA) on 85 structural and topological variables of 166 coded and non-coded amino acids. By using partial least squares (PLS), we applied VSTPV for the study of quantitative structure-activity models (QSARs) studies on two peptide panels as 101 synthetic cationic Antimicrobial polypeptides (CAMELs), and 28 bovine lactoferricin- (17 � 31)-pentadecapeptides (LFB). The results of QSARs models were superior to that of the earlier studies, with squared correlative coefficient R2 and cross-validated Q2 of 0.783, 0.656; and 0.864, 0.793, respectively. So, VSTPV descriptors were confirmed to be competent to extract information on 85 structural variables and to relate with biological activities.

Predicting the activity of ACE inhibitory peptides with a novel mode of pseudo amino acid composition.

In this study, physicochemical scale (P-scale), was recruited as a novel set of physicochemical descriptors derived from component analysis on four short of physicochemical properties variables (hydrophobic, electronic, steric and hydrogen bond contribution) of 20 coded amino acids, By using partial least squares (PLS), we applied P-scale for the study of quantitative structure activity relationship models (QASRs) on three angiotensin I converting enzyme (ACE) inhibitory peptides datasets (58 dipeptides, 55 tripeptides, and 50 tetrapeptides).The results of QSARs were superior to that of the earlier studies, with correlation coefficient (r(2)) and cross-validated(q(2)) equal to 0.902, 0.86; 0.985, 0.951 and 0.872, 0.77, respectively. By analysis, hydrophobic and steric properties of ACE-inhibitory peptide sequences play important roles in their bioactivities, and novel peptide sequence could be designed based on these properties of the amino acid residues. These results showed that P-scale descriptors can well represent the peptide sequence. Furthermore, the robust models show that P-scale descriptors can be further expanded for polypeptides and can serve as a useful quantitative tool for the rational drug design and discovery.

Molecular dynamics simulation of oseltamivir resistance in neuraminidase of avian influenza H5N1 virus.

The outbreak of avian influenza virus H5N1 has raised a global concern because of its high virulence and mutation rate. Although two classes of antiviral drugs, M2 ion channel protein inhibitors and neuraminidase inhibitors, are expected to be important in controlling the early stages of a potential pandemic. Different strains of influenza viruses have differing degrees of resistance against the antivirals. In order to analyze the detailed information on the viral resistance, molecular dynamics simulations were carried out for the neuraminidase (NA) complex with oseltamivir. The carboxylate of Glu276 of H252Y NA faces toward the O-ethyl-propyl group of oseltamivir, Glu276 of wild-type NA adopts a conformation pointing away from the oseltamivir. τ2 and τ3 torsional angles fluctuation of the oseltamivir are relatively high for the H252Y mutant NA complex. In addition, there are fewer hydrogen bonds between the oseltamivir and H252Y mutation NA. The results show that H252Y mutation NA has high resistance against the drug.

[Cloning of a phyA gene and its over expression in E. coli].

This research amplified the phyA gene with the designed and synthesized primers specific for the phyA gene full-length coding sequence. The phyA gene was from Aspergillus niger F246 by the polymerase chain reaction(PCR), which is selected and identified in our laboratory. After sequncing the coding sequence, it was confirmed that the construction of cloning vector was succeeded. The phyA gene fragment was recovered from the pMD18T-phyA and ligated with prokaryotic expression vector pET30a+ to construct the recombinant expression plasmid pET30a+ -phyA. It was expressed with IPTG induction in E. coli for high efficiency. A new protein band with apparent molecular weight 50 kDa was detected in the lysate of the transformed cell by using SDS-PAGE. The amount of the soluble fusion protein was about 40% of large intestine bacillus soluble protein of transformed cells, estimated by absorbance scanning of SDS-PAGE and protein quantitation. It's phytase activity was eight times over the natural phyase. So this research provides the basis of the study on obtaining large and high active phytase and developmant of the new microbial ecologicalagent.