title: High-throughput transcriptome sequencing analysis provides preliminary insights into the biotransformation mechanism of Rhodopseudomonas palustris treated with alpha-rhamnetin-3-rhamnoside.
abstract: BACKGROUND
  The purple photosynthetic bacterium Rhodopseudomonas palustris has been widely applied to enhance the therapeutic effects of traditional Chinese medicine using novel biotransformation technology. However, comprehensive studies of the R. palustris biotransformation mechanism are rare. Therefore, investigation of the expression patterns of genes involved in metabolic pathways that are active during the biotransformation process is essential to elucidate this complicated mechanism.
  
  
  RESULTS
  To promote further study of the biotransformation of R. palustris, we assembled all R. palustris transcripts using Trinity software and performed differential expression analysis of the resulting unigenes. A total of 9725, 7341 and 10,963 unigenes were obtained by assembling the alpha-rhamnetin-3-rhamnoside-treated R. palustris (RPB) reads, control R. palustris (RPS) reads and combined RPB&RPS reads, respectively. A total of 9971 unigenes assembled from the RPB&RPS reads were mapped to the nr, nt, Swiss-Prot, Gene Ontology (GO), Clusters of Orthologous Groups (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (E-value <0.00001) databases using BLAST software. A total of 3360 unique differentially expressed genes (DEGs) in RPB versus RPS were identified, among which 922 unigenes were up-regulated and 2438 were down-regulated. The unigenes were mapped to the KEGG database, resulting in the identification of 7676 pathways among all annotated unigenes and 2586 pathways among the DEGs. Some sets of functional unigenes annotated to important metabolic pathways and environmental information processing were differentially expressed between the RPS and RPB samples, including those involved in energy metabolism (18.4% of total DEGs), carbohydrate metabolism (36.0% of total DEGs), ABC transport (6.0% of total DEGs), the two-component system (8.6% of total DEGs), cell motility (4.3% of total DEGs) and the cell cycle (1.5% of total DEGs). We also identified 19 transcripts annotated as hydrolytic enzymes and other enzymes involved in ARR catabolism in R. palustris.
  
  
  CONCLUSIONS
  We present the first comparative transcriptome profiles of RPB and RPS samples to facilitate elucidation of the molecular mechanism of biotransformation in R. palustris. Furthermore, we propose two putative ARR biotransformation mechanisms in R. palustris. These analytical results represent a useful genomic resource for in-depth research into the molecular basis of biotransformation and genetic modification in R. palustris.
authors.affiliation: School of Pharmacy, Shanxi Medical University, Taiyuan 030001, PR China.
authors.forename: Lei
authors.initials: L
authors.lastname: Bi
authors.affiliation: School of Pharmacy, Shanxi Medical University, Taiyuan 030001, PR China.
authors.forename: Chun-jie
authors.initials: CJ
authors.lastname: Guan
authors.affiliation: School of Pharmacy, Shanxi Medical University, Taiyuan 030001, PR China. Electronic address: yangguane@aliyun.com.
authors.forename: Guan-e
authors.initials: GE
authors.lastname: Yang
authors.affiliation: School of Pharmacy, Shanxi Medical University, Taiyuan 030001, PR China.
authors.forename: Fei
authors.initials: F
authors.lastname: Yang
authors.affiliation: School of Pharmacy, Shanxi Medical University, Taiyuan 030001, PR China.
authors.forename: Hong-yu
authors.initials: HY
authors.lastname: Yan
authors.affiliation: School of Pharmacy, Shanxi Medical University, Taiyuan 030001, PR China.
authors.forename: Qing-shan
authors.initials: QS
authors.lastname: Li
mesh_terms: D001483:Base Sequence; D001711:Biotransformation / Q000187:drug effects; D002465:Cell Movement / Q000187:drug effects / Q000235:genetics; D030562:Databases, Protein; D015536:Down-Regulation; D015964:Gene Expression Regulation, Bacterial; D006027:Glycosides / Q000494:pharmacology*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D053858:Metabolic Networks and Pathways; D011794:Quercetin / Q000031:analogs & derivatives* / Q000737:chemistry / Q000494:pharmacology; D012241:Rhodopseudomonas / Q000187:drug effects / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D006027:Glycosides; C063423:rhamnetin; D011794:Quercetin
keywords: Alpha-rhamnetin-3-rhamnoside; Biotransformation; Rhodopseudomonas palustris; Transcriptome