title: Genomic and molecular mechanisms for efficient biodegradation of aromatic dye.
abstract: Understanding the molecular mechanisms for aromatic compound degradation is crucial for the development of effective bioremediation strategies. We report the discovery of a novel phenomenon for improved degradation of Direct Red 5B azo dye by Irpex lacteus CD2 with lignin as a co-substrate. Transcriptomics analysis was performed to elucidate the molecular mechanisms of aromatic degradation in white rot fungus by comparing dye, lignin, and dye/lignin combined treatments. A full spectrum of lignin degradation peroxidases, oxidases, radical producing enzymes, and other relevant components were up-regulated under DR5B and lignin treatments. Lignin induced genes complemented the DR5B induced genes to provide essential enzymes and redox conditions for aromatic compound degradation. The transcriptomics analysis was further verified by manganese peroxidase (MnP) protein over-expression, as revealed by proteomics, dye decolorization assay by purified MnP and increased hydroxyl radical levels, as indicated by an iron reducing activity assay. Overall, the molecular and genomic mechanisms indicated that effective aromatic polymer degradation requires synergistic enzymes and radical-mediated oxidative reactions to form an effective network of chemical processes. This study will help to guide the development of effective bioremediation and biomass degradation strategies.
authors.affiliation: School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China; Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Veterinary Pathology, Texas A&M University, College station, TX, USA.
authors.forename: Su
authors.initials: S
authors.lastname: Sun
authors.affiliation: School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China; Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.
authors.forename: Shangxian
authors.initials: S
authors.lastname: Xie
authors.affiliation: Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.
authors.forename: Hu
authors.initials: H
authors.lastname: Chen
authors.affiliation: Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.
authors.forename: Yanbing
authors.initials: Y
authors.lastname: Cheng
authors.affiliation: Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Shi
authors.affiliation: School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Qin
authors.affiliation: Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Veterinary Pathology, Texas A&M University, College station, TX, USA.
authors.forename: Susie Y
authors.initials: SY
authors.lastname: Dai
authors.affiliation: School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China. Electronic address: zhangxiaoyu@mail.hust.edu.cn.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zhang
authors.affiliation: School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China; Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA. Electronic address: syuan@tamu.edu.
authors.forename: Joshua S
authors.initials: JS
authors.lastname: Yuan
mesh_terms: D001391:Azo Compounds / Q000378:metabolism*; D001673:Biodegradation, Environmental; D016000:Cluster Analysis; D023281:Genomics; D007501:Iron / Q000378:metabolism; D008031:Lignin / Q000378:metabolism; D010084:Oxidation-Reduction; D010544:Peroxidases / Q000378:metabolism; D020072:Polyporales / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D001391:Azo Compounds; C542892:Direct Red 5B; D008031:Lignin; D007501:Iron; D010544:Peroxidases; C051129:manganese peroxidase
keywords: Azo dye; Mechanism; Molecular; Transcriptomics; White rot fungi