Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes

Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging.In this study,we developed a sequence-based functional metagenomics procedure for mining the diversity of copper(Cu)resistance gene copA in global microbiomes,by combining the metagenomic assembly technology,local BLAST,evolutionary trace analysis(ETA),chemical synthesis,and conventional functional genomics.In total,87 metagenomes were collected from a public database and subjected to copA detection,resulting in 93,899 hits.Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates,which were further subjected to ETA.Eventually,175 novel copA sequences of high quality were discovered.Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins,with 55 sequences from totally unknown species.Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli(DcopA).The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake.One recombinant harboring copA-like 15(copAL15)successfully restored Cu resistance of the host with a substantially enhanced Cu uptake.Two novel copA genes were fused with the gfp gene and expressed in E.coli for microscopic observation.Imaging results showed that they were successfully expressed and their proteins were localized to the membrane.The results here greatly expand the diversity of known CopA proteins,and the sequence-based procedure developed overcomes biases in length,screening methods,and abundance of conventional functional metagenomics.

Diversity of insect communities with different development phases in natural Populus euphratica forests in Xinjiang

An investigation method with sample plots was used to study insect communities in four different growth phases of natural Populus euphratica forests, which are juvenile, middle aged, over-mature and degraded forests, in Tarim, Xinjiang in July, 2005 and April, 2006. In our studies, 5,116 insect specimens, belonging to 12 orders, 61 families and 141 species, were collected. Lepidoptera and Coleoptera were the dominant orders. In middle-aged forests, species, individual numbers and diversity indices of insect com-munities were higher than those in other woodlands. The species richness and diversity indices were lowest in degraded forests be-cause of extremely scarce vegetation.

Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex

While the structures of plant primary metabolic pathways are generally well defined and highly conserved across species,those defining specialized metabolism are less well characterized and more highly variable across species.In this study,we investigated polyphenolic metabolism in the lycopersicum complex by characterizing the underlying biosynthetic and decorative reactions that constitute the metabolic network of polyphenols across eight different species of tomato.For this purpose,GC-MS-and LC-MS-based metabolomics of different tissues of Solatium lycopersicum and wild tomato species were carried out,in concert with the evaluation of cross-hybridized microarray data for MapMan-based transcriptomic analysis,and publicly available RNA-sequencing data for annotation of biosynthetic genes.The combined data were used to compile species-specific metabolic networks of polyphenolic metabolism,allowing the establishment of an entire pan-species biosynthetic framework as well as annotation of the functions of decoration enzymes involved in the formation of metabolic diversity of the flavonoid pathway.The combined results are discussed in the context of the current understanding of tomato flavonol biosynthesis as well as a global view of metabolic shifts during fruit ripening.Our results provide an example as to how large-scale biology approaches can be used for the definition and refinement of large specialized metabolism pathways.