Chlamydiae has contributed at least 55 genes to plantae with predominantly plastid functions

PLoS ONE

Volumn 3, Issue 5, 2008, Pages

  Moustafa, Ahmed ^a   Reyes Prieto, Adrian ^a   Bhattacharya, Debashish ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE; BISPHOSPHOGLYCERATE MUTASE; CARBONATE DEHYDRATASE II; COPPER ZINC SUPEROXIDE DISMUTASE; CYTIDINE DEAMINASE; DEOXYCYTIDINE PHOSPHATE DEAMINASE; DEXTRO ALANINE DEXTRO ALANINE LIGASE; EXONUCLEASE; GLYCEROL 3 PHOSPHATE ACYLTRANSFERASE; GLYCOSYLTRANSFERASE; IRON SUPEROXIDE DISMUTASE; ISOAMYLASE; ISOMERASE; LEUCINE RICH REPEAT KINASE 2; MALATE DEHYDROGENASE; MANGANESE SUPEROXIDE DISMUTASE; METHYLTRANSFERASE; PHOSPHATE TRANSPORTER; PHOSPHOGLYCERATE MUTASE; POLYPHOSPHOINOSITIDE; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; PSEUDOURIDINE; RIBOSOME PROTEIN; RNA BINDING PROTEIN; RNA METHYLTRANSFERASE; THIOSULFATE SULFURTRANSFERASE; TRANSFER RNA METHYLTRANSFERASE; URIDINE DIPHOSPHATE GLUCOSE 4 EPIMERASE;

ACANTHAMOEBA; AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; BIOGENESIS; CANDIDATUS PROTOCHLAMYDIA AMOEBOPHILA; CELL FUNCTION; CELL METABOLISM; CHLAMYDIA; ENDOSYMBIOSIS; EVOLUTION; GENE FUNCTION; GENE IDENTIFICATION; GENE TRANSFER; GENOME; MITOCHONDRION; NONHUMAN; PHYLOGENY; PLASTID; PROTEIN LOCALIZATION; SEQUENCE HOMOLOGY; GENETICS; MICROBIOLOGY; PLANT;

ACANTHAMOEBA; ALGAE; CANDIDATUS PROTOCHLAMYDIA AMOEBOPHILA; CHLAMYDIAE; EMBRYOPHYTA; GLAUCOCYSTOPHYCEAE; PLANTAE; PROTISTA;

CHLAMYDIA; GENES, BACTERIAL; PLANTS; PLASTIDS;

EID: 48249125417     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0002205     Document Type: Article

References (52)

1. Bhattacharya D, Yoon HS, Hackett JD (2004) Photosynthetic eukaryotes unite: endosymbiosis connects the dots. Bioessays 26: 50-60.
2. Cavalier-Smith T (2002) The phagotrophic origin of eukaryotes and phylogenetic classification ofProtozoa. Int J Syst Evol Microbiol 52: 297-354.
3. Adl SM, Simpson AG, Farmer MA, Andersen RA, Anderson OR, et al. (2005) The new higher level classification ofeukaryotes with emphasis on the taxonomy of protisis. J Eukaryot Microbiol 52: 399-451.
4. Simpson AG, Roger AJ (2004) ne real 'kingdonis' of eukaryotes. Curr Biol 14: R693-696.
5. Delwiche CF (1999) Tracing the Thread or Plastid Diversity through the Tapestry of Life. Am Nat 154: S164-S177.
6. Hackett JD, Yoon HS, Li S, Reyes-Prieto A, Rummele SE, et al. (2007) Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Mol Biol Evol 24: 1702-1713.
7. Rodriguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, et al. (2005) Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr Biol 15: 1325-1330.
8. Nozaki H, Iseki M, Hasegawa M, Misawa K, Nakada T, et al. (2007) Phylogeny of primary photosynthetic eukaryotes as deduced from slowly evolving nuclear genes. Mol Biol Evol 24: 1592-1595.
9. Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, et al. (2006) Evaluating support for the current classification of cukaryotic diversity. PLoS Genet 2: e220.
10. Falkowski PG, Katz ME, Knoll AH, Quigg A, Raven JA, et al. (2004) The evolution of modern eukaryotic phytoplankton. Science 305: 354-360.
11. Bhattacharya D, Archibald JM, Weber AP, Reyes-Prieto A (2007) How do endosymbionts become organelles? Understanding early events in plastid evolution. Bioessays 29: 1239-1246.
12. Martin W, Stoebe B, Goremykin V, Hapsmann S, Hasegawa M, et al. (1998) Gene transfer to the nucleus and the evolution of chloroplasis. Nature 393: 162-165.
13. McFadden GI, van Dooren GG (2004) Evolution: red algal genome affirms a common origin of all plastids. Curr Biol 14: R514-516.
14. Reyes-Prieto A, Weber AP, Bhattacharya D (2007) The origin and establishment or the plastid in algae and plants. Annu Rev Genet 41: 147-168.
15. Brinkman FS, Blanchard JL, Cherkasov A, Av-Gay Y, Brunham RC, et al. (2002) Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamvdiaceae, cyanobacteria, and the chloroplast. Genome Res 12: 1159-1167.
16. Corsaro D, Greub G (2006) Pathogenic potential of novel Chlamydiae and diagnostic approaches to infections due to these obligate intracellular bacteria. Clin Microbiol Rev 19: 283-297.
17. Greub G, Raoult D (2003) History of the ADP/ATP-translocase-encoding gene, a parasitism gene transferred from a Chlamydiales ancestor to plants 1 billion years ago. Appl Environ Microbiol 69: 5530-5535.
18. Horn M, Collingro A, Schmitz-Esser S, Beier CL, Purkhold U, et al. (2004) Illuminating the evolutionary history of chlamydiae. Science 304: 728 730.
19. Stephens RS, Kalman S, Lammel C, Fan J, Marathe R, et al. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 282: 754-759.
20. Everett KD, Thao M, Horn M, Dyszynski GE, Baumann P (2005) Novel chlamydiae in whitellies and scale insects: endosymbionts 'Candidalus Fritschea bemisiae' strain Falk and 'Candidalus Fritschen eriococci' strain Elm. Int J Syst Evol Microbiol 55: 1581-1587.
21. Tyra HM, Linka M, Weber AP, Bhattacharya D (2007) Host origin of plastid solute transporters in the first photosynthetic eukaryotes. Genome Biol 8: R212.
22. Huang J, Gogarten JP (2007) Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biol 8: R99.
23. Moustafa A, Bhattacharya D (2008) PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas. BMC Evol Biol 8: 6.
24. Doolittle WF (1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 14: 307-311.
25. Stechmann A, Baumgartner M, Silberman JD, Roger AJ (2006) The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic. BMC Evol Biol 6: 101.
26. Schmitz-Esser S, Linka N, Collingro A, Beier CL, Neuhaus HE, et al. (2004) ATP/ADP translocases: a common feature of obligate intracellular amoebal symbionts related to Chlamydiae and Rickettsiae. J Bacteriol 186: 683-691.
27. Siamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
28. Emanuelsson O, Nielsen H, Brunak S, von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016.
29. Small I, Peeters N, Legeai F, Lurin C (2004) Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4: 1581-1590.
30. Emanuelsson O, Nielsen H, von Heijne G (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci 8: 978-984.
31. Chang JM, So EC, Lo A, Chiu HS, Sung TY, et al. (2008) PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis. Proteins.
32. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, et al. (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35: W585-587.
33. Matsuzaki M, Misumi O, Shin IT, Maruyama S, Takahara M, et al. (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428: 653-657.
34. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318: 245-250.
35. Tokuhisa JG, Vijayan P, Feldmann KA, Browse JA (1998) Chloroplast development at low temperatures requires a homolog of DIM1, a yeast gene encoding the 18S rRNA dimethylase. Plant Cell 10: 699-711.
36. Guindon S, Lethiec F, Duroux P, Gascuel O (2005) PHYML Online a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33: W557-559.
37. Deusch O, Lanclan G, Roettger M, Gruenheit N, Kowallik KV, et al. (2008) Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor. Mol Biol Evol 25: 748-761.
38. Christie PJ, Vogel JP (2000) Bacterial type IV secretion: conjugation systems adapted to deliver effector molecules to host cells. Trends Microbiol 8: 354-360.
39. Greub G, Collyn F, Guy L, Roten CA (2004) A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system. BMG Microbiol 4: 48.
40. Reyes-Prieto A, Hackett JD, Soares MB, Bonaldo MF, Bhauacharya D (2006) Cyanobacterial contribution to algal nuclear genomes is primarily limited to plastid functions. Curr Biol 16: 2320-2325.
41. Leister D (2005) Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends Genet 21: 635-663.
42. Thorsness PE, Weber ER (1996) Escape and migration of nucleic acids between chloroplasts, mitochondria, and the nucleus. Int Rev Cytol 165: 207-234.
43. Nosenko T, Bhattacharya D (2007) Horizontal gene transfer in chromalveolates. BMC Evol Biol 7: 173.
44. Watkins RF, Gray MW (2006) The frequency of eubacterium-to-eukaryote lateral gene transfers shows significant cross-taxa variation within amoebozoa. J Mol Evol 63: 801-814.
45. Huang CY, Grunheit N, Ahmadinejad N, Timmis JN, Martin W (2005) Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes. Plant Physiol 138: 1723-1733.
46. Matsuo M, Ito Y, Yamauchi R, Obokata J (2005) The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux. Plant Cell 17: 665-675.
47. Brennicke A, Grohmann L, Hiesel R, Knoop V, Schuster W (1993) The mitochondrial genome on its way to the nucleus: different stages of gene transfer in higher plants. FEBS Lett 325: 140-145.
48. Martin W, Herrmann RG (1998) Gene transfer from organelles to the nucleus: how much, what happens, and Why? Plant Physiol 118: 9-17.
49. Muller HJ (1964) The Relation of Recombination to Mutational Advance. Mutat Res 106: 2-9.
50. Frickey T, Lupas AN (2004) PhyloGenie: automated phylome generation and analysis. Nucleic Acids Res 32: 5231-5238.
51. Boguski MS, Iowe TM, Tolstushev CM (1993) dbEST database for "expressed sequence tags". Nat Genet 4: 332-333.
52. O'Brien EA, Koski LB, Zhang Y, Yang L, Wang E, et al. (2007) TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). Nucleic Acids Res 35: D445-451.