title: In silico analysis of phytoene synthase and its promoter reveals hints for regulation mechanisms of carotenogenesis in Duanliella bardawil.
abstract: BACKGROUND
  Previous researches showed that phytoene synthase (Psy) from Dunaliella bardawil is the first regulatory point in carotenogenesis. We hypothesize certain interactions between the environmental stress factors and the regulatory sequences of Psy in D.bardawil (DbPsy). Consequently, LA PCR-based genomic walking approach was performed for isolation of psy promoter and terminator, respectively. The obtained nucleic acid sequences and the corresponding protein structure of DbPsy were analyzed and predicted using various bioinformatics tools. Finally, we presented some hints for the regulation mechanisms of DbPsy at the molecular level according to the computed results.
  
  
  RESULTS
  LA PCR-based genomic walking results showed that the isolated sequences are the promoter and terminator of psy, correspondingly. Computational analysis demonstrated several candidate motifs of the promoter exhibiting hypothetic UV-B-, norglurzon- and salt-induced characteristics, as well as some typical domains universally discovered in promoter sequences, such as TATA-box, CCAAT-box and GATA-box, etc. Furthermore, the structure of Psy was also predicted and aligned along with many counterparts at the protein level. Low homology of N-terminus was found in D.bardawil, while a relatively conserved C-terminus was predicted to be involved in the catalytic activity and substrate recognization/binding. Phylogenic analysis classified the DbPsy into a cluster with other algae. These results implied that Psy may share similar regulation mechanisms among algae with respect to their C-termini; while the diversity in N-terminus among Psys, along with the predicted inducible motifs in psy promoter from D.bardawil, may confer the fine tuning differences between D.bardawil and other algae.
  
  
  CONCLUSIONS
  By means of computer techniques, we found in D.barawali that two interesting conserved motifs of psy promoter may involve in UV-B, norglurzon and salt regulation correspondingly; and that the diversity of Psy protein mainly lies in the N-termini among algae. These results indicate some hints for regulation mechanisms of carotenogenesis in D.bradawil.
  
  
  BACKGROUND
  jgjiang@scut.edu.cn.
authors.affiliation: College of Food and Bioengineering, South China University of Technology, Guangzhou, 510640, China.
authors.forename: Yong-Min
authors.initials: YM
authors.lastname: Lao
authors.forename: Lan
authors.initials: L
authors.lastname: Xiao
authors.forename: Zhi-Wei
authors.initials: ZW
authors.lastname: Ye
authors.forename: Jian-Guo
authors.initials: JG
authors.lastname: Jiang
authors.forename: Shi-Shui
authors.initials: SS
authors.lastname: Zhou
mesh_terms: D019883:Alkyl and Aryl Transferases / Q000737:chemistry / Q000235:genetics*; D000595:Amino Acid Sequence; D002338:Carotenoids / Q000096:biosynthesis; D000460:Chlorophyta / Q000235:genetics* / Q000378:metabolism; D018076:DNA, Complementary / Q000737:chemistry; D018506:Gene Expression Regulation, Plant; D051232:Geranylgeranyl-Diphosphate Geranylgeranyltransferase; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics*; D011401:Promoter Regions, Genetic; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013728:Terminator Regions, Genetic
chemical_list: D018076:DNA, Complementary; D010940:Plant Proteins; D002338:Carotenoids; D019883:Alkyl and Aryl Transferases; D051232:Geranylgeranyl-Diphosphate Geranylgeranyltransferase