title: Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum.
abstract: BACKGROUND
  DNA gyrase, an enzyme once thought to be unique to bacteria, is also found in some eukaryotic plastids including the apicoplast of Apicomplexa such as Plasmodium falciparum and Toxoplasma gondii which are important disease-causing organisms. DNA gyrase is an excellent target for antibacterial drugs, yet such antibacterials seem ineffective against Apicomplexa. Characterisation of the apicoplast gyrases would be a useful step towards understanding why this should be so. While purification of active apicoplast gyrase has proved impossible to date, in silico analyses have allowed us to discover differences in the apicoplast proteins. The resulting predicted structural and functional differences will be a first step towards development of apicoplast-gyrase specific inhibitors.
  
  
  RESULTS
  We have carried out sequence analysis and structural predictions of the enzymes from the two species and find that P. falciparum gyrase lacks a GyrA box, but T. gondii may retain one. All proteins contained signal/transport peptides for localization to the apicoplast but T. gondii Gyrase B protein lacks the expected hydrophobic region. The most significant difference is in the GyrA C-terminal domain: While the cores of the proteins, including DNA binding and cleavage regions are essentially unchanged, both apicoplast gyrase A proteins have C-terminal domains that are significantly larger than bacterial counterparts and are predicted to have different structures.
  
  
  CONCLUSIONS
  The apicoplast gyrases differ significantly from bacterial gyrases while retaining similar core domains. T. gondii Gyrase B may have an unusual or inefficient mechanism of localisation to the apicoplast. P.falciparum gyrase, lacks a GyrA box and is therefore likely to be inefficient in DNA supercoiling. The C-terminal domains of both apicoplast Gyrase A proteins diverge significantly from the bacterial proteins. We predict that an additional structural element is present in the C-terminal domain of both apicoplast Gyrase A proteins, including the possibility of a β-pinwheel with a non-canonical number of blades. These differences undoubtedly will affect the DNA supercoiling mechanism and have perhaps evolved to compensate for the lack of Topoisomerase IV in the apicoplast. These data will be useful first step towards further characterisation and development of inhibitors for apicoplast gyrases.
authors.affiliation: Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. nagano.soshichiro@gmail.com.
authors.forename: Soshichiro
authors.initials: S
authors.lastname: Nagano
authors.affiliation: Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. ting-yu.lin@riken.jp.
authors.forename: Ting-Yu
authors.initials: TY
authors.lastname: Lin
authors.affiliation: Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. jyotheeswara@biken.osaka-u.ac.jp.|Current address: Department of Molecular Protozoology, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan. jyotheeswara@biken.osaka-u.ac.jp.
authors.forename: Jyotheeswara Reddy
authors.initials: JR
authors.lastname: Edula
authors.affiliation: Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. heddle@riken.jp.
authors.forename: Jonathan Gardiner
authors.initials: JG
authors.lastname: Heddle
mesh_terms: D000595:Amino Acid Sequence; D063546:Apicoplasts / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry; D001692:Biological Transport; D003198:Computer Simulation; D027081:DNA Gyrase / Q000737:chemistry*; D005326:Fetal Proteins / Q000737:chemistry; D006801:Humans; D016778:Malaria, Falciparum / Q000201:enzymology* / Q000235:genetics / Q000469:parasitology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010963:Plasmodium falciparum / Q000201:enzymology* / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D020825:T-Box Domain Proteins / Q000737:chemistry; D014122:Toxoplasma / Q000201:enzymology* / Q000235:genetics; D000098908:Brachyury Protein
chemical_list: D001426:Bacterial Proteins; D027081:DNA Gyrase; D005326:Fetal Proteins; D020825:T-Box Domain Proteins; D000098908:Brachyury Protein