title: A newly discovered ubiquitin-conjugating enzyme E2 correlated with the cryogenic autolysis of Volvariella volvacea.
abstract: In Volvariella volvacea, a species of edible mushroom, cryogenic autolysis is a typical part of abnormal metabolism. Previous functional annotation cluster analyses of cold-induced gene expression profiles have shown that the ubiquitin-conjugating enzyme E2 (UBE2), rather than the cyclin-like F-box domain alone, forms the functional cluster. In this study, analysis of gene expression profiling showed that only one type of UBE2 in V. volvacea (UBEV2) was significantly up-regulated. Further quantitative real-time PCR analysis confirmed that the expression of UBEV2 was significantly up-regulated (P<0.05) after cold-treatment lasting 4, 6, and 8h. This provided evidence that UBEV2 was closely correlated with cryogenic autolysis. The specific distribution of UBEV2 in recently diverged herb decay fungi indicated that UBEV2 was not evolutionarily correlated with early diverging fungi. Phylogenetic analysis indicated that UBEV2 was generated by horizontal gene transfer (HGT) from the ancestry of Selaginella moellendorffii UBE2. Further relative time estimation and detection of natural selection showed that there has been recent positive selection after HGT in UBEV2. Molecular modeling and logo analysis showed that the cysteine-cysteine motif is the characteristic of the UBEV2 family. These observations indicate that UBEV2 is a new type of UBE2 correlated with the cryogenic autolysis of V. volvacea.
authors.affiliation: National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China; Department of Computer Science, University of Nebraska at Omaha, Omaha, NE 68182, USA.
authors.forename: Ming
authors.initials: M
authors.lastname: Gong
authors.affiliation: National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China.
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.affiliation: National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China.
authors.forename: Mingjie
authors.initials: M
authors.lastname: Chen
authors.affiliation: National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China.
authors.forename: Dapeng
authors.initials: D
authors.lastname: Bao
authors.affiliation: Department of Computer Science, University of Nebraska at Omaha, Omaha, NE 68182, USA. Electronic address: qzhu@mail.unomaha.edu.
authors.forename: Qiuming
authors.initials: Q
authors.lastname: Zhu
authors.affiliation: National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China. Electronic address: tanqsaas@gmail.com.
authors.forename: Qi
authors.initials: Q
authors.lastname: Tan
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D022761:Gene Transfer, Horizontal; D008969:Molecular Sequence Data; D010802:Phylogeny; D012641:Selection, Genetic; D044763:Ubiquitin-Conjugating Enzymes / Q000235:genetics* / Q000378:metabolism*; D055367:Volvariella / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*
chemical_list: D005656:Fungal Proteins; D044763:Ubiquitin-Conjugating Enzymes
keywords: Abnormal metabolism; Autolysis; Horizontal gene transfer; Ubiquitin-conjugating enzyme E2; Volvariella volvacea