Hybrid pseudomonads engineered by two-step homologous recombination acquire novel degradation abilities toward aromatics and polychlorinated biphenyls

Discovery by metagenomics of a functional tandem repeat sequence that controls gene expression in bacteria

The ability to degrade exogenous compounds is acquired by adaptive processes of microorganisms when they are exposed to compounds that are foreign to their existing enzyme systems. Previously, we reported that simultaneous point mutations and mobile genetic elements cause the evolution and optimization of the degradation systems for aromatic compounds. In the present study, we propose another element with this role—tandem repeats. The novel metagenomic tandem repeat (MTR) sequence T(G/A)ACATG(A/C)T was identified in the 5′-untranslated regions of catechol 2,3-dioxygenase (C23O)-encoding genes by metagenomic analysis. Recombinant Escherichia coli carrying a C23O gene with various numbers of MTRs exhibited increased C23O protein expression and enzyme activity compared with cells expressing the C23O gene without MTRs. Real-time reverse transcription-PCR showed that changes in the numbers of MTRs affected the levels of detectable C23O mRNA in the E. coli host. Furthermore, the mRNAs transcribed from C23O genes containing various numbers of MTRs had longer half-lives than those transcribed from a C23O gene without MTRs. Thus, MTRs would affect the translation efficiency of the gene expression system. MTRs may change the expression levels of their downstream genes for adaptation to a fluctuating environment.

Phylloremediation of Air Pollutants: Exploiting the Potential of Plant Leaves and Leaf-Associated Microbes

Air pollution is air contaminated by anthropogenic or naturally occurring substances in high concentrations for a prolonged time, resulting in adverse effects on human comfort and health as well as on ecosystems. Major air pollutants include particulate matters (PMs), ground-level ozone (O3), sulfur dioxide (SO2), nitrogen dioxides (NO2), and volatile organic compounds (VOCs). During the last three decades, air has become increasingly polluted in countries like China and India due to rapid economic growth accompanied by increased energy consumption. Various policies, regulations, and technologies have been brought together for remediation of air pollution, but the air still remains polluted. In this review, we direct attention to bioremediation of air pollutants by exploiting the potentials of plant leaves and leaf-associated microbes. The aerial surfaces of plants, particularly leaves, are estimated to sum up to 4 × 108 km2 on the earth and are also home for up to 1026 bacterial cells. Plant leaves are able to adsorb or absorb air pollutants, and habituated microbes on leaf surface and in leaves (endophytes) are reported to be able to biodegrade or transform pollutants into less or nontoxic molecules, but their potentials for air remediation has been largely unexplored. With advances in omics technologies, molecular mechanisms underlying plant leaves and leaf associated microbes in reduction of air pollutants will be deeply examined, which will provide theoretical bases for developing leaf-based remediation technologies or phylloremediation for mitigating pollutants in the air.

Diversity of extradiol dioxygenases in aromatic-degrading microbial community explored using both culture-dependent and culture-independent approaches

Culture-dependent and culture-independent approaches were used for extensive retrieval of the extradiol dioxygenase (EDO) gene from the environment to investigate the relationship between the EDO genes from isolated bacteria and the metagenomic EDO genes from which they were isolated. In our previous study, we identified 91 fosmid clones showing EDO enzyme activity using a metagenomic approach. In the present study, we classified all these metagenome-derived EDOs and newly isolated 88 phenol-utilizing bacteria from the same sample and identified four EDO genes from them. Of these, two EDOs had amino acid sequences similar to those reported previously in aromatic-utilizing strains, and one EDO had a sequence almost identical to that of metagenomic EDOs identified in our previous study. Unexpectedly, one EDO showed no similarity to any class I EDOs and was categorized as class II, which has not been found in past metagenomic approaches. Quantitative polymerase chain reaction (PCR) assay indicated that the low-abundance class II EDO gene can be enriched by culturing approaches. We conclude that the combined use of the two approaches can explore the gene community more extensively than their individual use.