Understanding Lignin-Degrading Reactions of Ligninolytic Enzymes: Binding Affinity and Interactional Profile

Previous works have demonstrated that ligninolytic enzymes mediated effective degradation of lignin wastes. The degrading ability greatly relied on the interactions of ligninolytic enzymes with lignin. Ligninolytic enzymes mainly contain laccase (Lac), lignin peroxidase (LiP) and manganese peroxidase (MnP). In the present study, the binding modes of lignin to Lac, LiP and MnP were systematically determined, respectively. Robustness of these modes was further verified by molecular dynamics (MD) simulations. Residues GLU460, PRO346 and SER113 in Lac, residues ARG43, ALA180 and ASP183 in LiP and residues ARG42, HIS173 and ARG177 in MnP were most crucial in binding of lignin, respectively. Interactional analyses showed hydrophobic contacts were most abundant, playing an important role in the determination of substrate specificity. This information is an important contribution to the details of enzyme-catalyzed reactions in the process of lignin biodegradation, which can be used as references for designing enzyme mutants with a better lignin-degrading activity

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The genome of the sea squirt Ciona Intestinalis: The seeds of vertebrate innovation

The first chordates appeared over a half a billion years ago, providing the ancestral stock from which modern vertebrates emerged. To shed some light on the chordate origins, we have sequenced the genome of Ciona intestinalis, a sea squirt whose lineage split from that of vertebrates in the mid Cambrian. Ciona has long been a popular model system for the study of development, featuring world-wide and year-round availability, easily visualized cells and morphogenetic processes, simple methods for transient transgene expression, and a growing genomic infrastructure including extensive EST and cDNA collections. A comparison of the assembled Ciona genome sequence and gene complement with available invertebrate and vertebrate sequences provides insight into the origins and development of a chordate and vertebrate systems including the nervous systems, muscular, immune and endocrine systems, as well as the evolution of the chordate body plan. The Ciona genome provides a foundation for a genome-scale analyses of regulatory networks through chordate development