Predicted secondary structure of the foraminiferal SSU 3′ major domain reveals a molecular synapomorphy for granuloreticulosean protists

Journal of Eukaryotic Microbiology

Volumn 51, Issue 4, 2004, Pages 464-471

  Habura, Andrea ^a   Rosen, Daniel R ^a,b   Bowser, Samuel S ^a,b  

^a WADSWORTH CENTER   (United States)

^b STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

Foraminifera; Molecular phylogeny; Ribosomal inserts; Ribosomal RNA; Taxonomy

Indexed keywords

PROTOZOAL RNA; RIBOSOME RNA;

PHYLOGENETICS;

ANIMAL; ARTICLE; CHEMISTRY; CONFORMATION; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTOZOON; RIBOSOME; SEQUENCE HOMOLOGY;

ANIMALS; BASE SEQUENCE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTOZOA; RIBOSOMES; RNA, PROTOZOAN; RNA, RIBOSOMAL; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ANIMALIA; EUKARYOTA; FORAMINIFERA; GRANULORETICULOSEA; PROTISTA; PROTOZOA;

EID: 3242888291     PISSN: 10665234     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1550-7408.2004.tb00397.x     Document Type: Article

References (47)

1. Archibald, J. M., Longet, D., Pawlowski, J. & Keeling, P. J. 2003. A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol. Biol. Evol., 20:62-66.
2. Arnold, Z. 1948. A new foraminiferan belonging to the genus Allogromia. Trans. Amer. Micr. Soc., 67:231-235.
3. Bowser, S. S. & DeLaca, T. E. 1985. Rapid intracellular motility and dynamic membrane events in an Antarctic foraminifer. Cell Biol. Int. Rep., 9:901-909.
4. Bowser, S. S. & Travis, J. L. 2002. Reticulopodia: structural and behavioral basis for the suprageneric placement of Granuloreticulosan protists. J. Foram. Res., 32:440-447.
5. Bowser, S. S., Bernhard, J. M., Habura, A. & Gooday, A. J. 2002. Structure, taxonomy and ecology of Astrammina triangularis (Earland), an allogromiid-like agglutinated foraminifer from Explorers Cove, Antarctica. J. Foram. Res., 32:364-374.
6. Cannone, J. J., Subramanian, S., Schnare, M. N., Collett, J. R., D'Souza, L. M., Du, Y., Feng, B., Lin, N., Madabusi, L. V., Müller, K. M., Pande, N., Shang, Z., Yu, N. & Gutell, R. R. 2002. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3:2.
7. Cavalier-Smith, T. 2002. The phagotrophic origin of eukaryotes and phylogenetic classification of protozoa. Int. J. Syst. Evol. Microbiol., 52:297-354.
8. Cedhagen, T., Goldstein, S. & Gooday A. 2002. A theme issue on the biology and biodiversity of "Allogromiid" foraminifera. J. Foram. Res., 32:331-333.
9. Cole, J. R., Chai, B., Marsh, T. L., Farris, R. J., Wang, Q., Kulam, S. A., Chandra, S., McGarrell, D. M., Schmidt, T. M., Garrity, G. M. & Tiedje, J. M. 2003. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucl. Acids Res., 31:442-443.
10. Crease, T. J. & Colbourne, J. K. 1998. The unusually long small-subunit ribosomal RNA of the crustacean, Daphnia pulex: sequence and predicted secondary structure. J. Mol. Evol., 46:307-313.
11. Culver, S. J. 1991. Early Cambrian Foraminifera from West Africa. Science, 254:689-691.
12. Dacks, J. B. & Doolittle, W. F. 2001. Reconstructing/deconstructing the earliest eukaryotes: how comparative genomics can help. Cell, 107: 419-425.
13. DeLaca, T. 1986. The morphology and ecology of Astrammina rara. J. Foram. Res., 16:216-223.
14. De Rijk, P. & De Wachter, R. 1997. RnaViz, a program for the visualisation of RNA secondary structure. Nucl. Acids Res., 25:4679-4684.
15. de Vargas, C., Renaud, S., Hilbrecht, H. & Pawlowski, J. 2001. Pleistocene adaptive radiation in Globorotalia truncatulinoides: genetic, morphologic, and environmental evidence. Paleobiology, 27:104-125.
16. Galtier, N., Gouy, M. & Gautier, C. 1996. SEAVIEW and PHYLO_WIN, two graphic tools for sequence alignment and molecular phylogeny. Comput. Applic. Biosci., 12:543-548.
17. Gooday, A. J., Bowser, S. S. & Bernhard, J. M. 1996. Benthic foraminiferal assemblages in Explorers Cove, Antarctica: a shallow-water site with deep-sea characteristics. Prog. Oceanog., 37:117-166.
18. Habura, A., Pawlowski, J., Hanes, S. D. & Bowser, S. S. 2004. Unexpected foraminiferal diversity revealed by small-subunit rDNA analysis of Antarctic sediment. J. Eukaryot. Microbiol., 51:173-179.
19. Hancock, J. M. & Vogler, A. P. 2000. How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: implications for phylogeny reconstruction. Mol. Phylog. Evol., 14:366-374.
20. Holzmann, M., Hohenegger, J., Hallock, P., Piller, W. E. & Pawlowski, J. 2001. Molecular phylogeny of large miliolid foraminifera (Soritacea Ehrenberg 1839). Mar. Micropal., 43:57-74.
21. Huber, B. T., Bijma, J. & Darling, K. 1997. Cryptic speciation in the living planktonic foraminifer Globigerinella siphonifera (d'Orbigny). Paleobiology, 23:33-62.
22. Keeling, P. J. 2001. Foraminifera and Cercozoa are related in actin phylogeny: Two orphans find a home? Mol. Biol. Evol., 18:1551-1557.
23. Knudsen, B. & Hein, J. J. 1999. Using stochastic context free grammars and molecular evolution to predict RNA secondary structure. Bioinformatics, 15:446-454.
24. Lee, J. J., Pawlowski, J., Debenay, J.-P., Whittaker, J., Banner, F., Gooday, A. J., Tendal, O., Haynes, J. & Faber, W. W. 2000. Phylum Granuloreticulosa. In: Lee, J. J., Leedale, G. F. & Bradbury, P. (ed.), Illustrated Guide to the Protozoa. 2nd. ed. Allen Press Inc., Lawrence. 2:872-951.
25. Loeblich, A. R. & Tappan, H. 1988. Foraminiferal Genera and their Classification, Vol. 1-2, Van Nostrand Reinhold, N.Y.
26. Longet, D., Archibald, J. M., Keeling, P. J. & Pawlowski, J. 2003. Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies. Int. J. Syst. Evol. Microbiol., 53:1735-1739.
27. Pawlowski, J. 2000. Introduction to the molecular systematics of foraminifera. Micropalentology, 46(Suppl. 1):1-12.
28. Pawlowski, J., Bolivar, I., Fahrni, J. F., Cavalier-Smith, T. & Gouy, M. 1996. Early origin of Floraminifera suggested by SSU rRNA gene sequences. Mol. Biol. Evol., 13:445-450.
29. Pawlowski, J., Fahrni, J., Brykczynska, U., Habura, A. & Bowser, S. S. 2002a. Molecular data reveal high taxonomic diversity of allogromiid Foraminifera in Explorers Cove (McMurdo Sound, Antarctica). Polar Biol., 25:96-105.
30. Pawlowski, J., Bolivar, I., Fahrni, J. F., de Vargas, C., Gouy, M. & Zaninetti, L. 1997. Extreme differences in rates of molecular evolution of Foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record. Mol. Biol. Evol., 14:498-505.
31. Pawlowski, J., Holzmann, M., Berney, C., Fahrni, J., Cedhagen, T., Habura, A. & Bowser, S. S. 2002b. Phylogeny of allogromiid Foraminifera inferred from SSU rRNA gene sequences. J. Foram. Res., 32:334-343.
32. Pawlowski, J., Holzmann, M., Berney, C., Fahrni, J., Gooday, A. J., Cedhagen, T., Habura, A. & Bowser, S. S. 2003. The evolution of early Foraminifera. Proc. Natl. Acad. Sci. USA, 100:11494-11498.
33. Sen Gupta, B. K. 1999. Modern Foraminifera. Kluwer Academic Publishers, Dordrecht, The Netherlands.
34. Sharma, M. R., Koc, E. C., Datta, P. P., Booth, T. M., Spremulli, L. L. & Agrawal, R. K. 2003. Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins. Cell, 115:97-108.
35. Simpson, A. G. B., Roger, A. J., Silberman, J. D., Leipe, D. D., Edgcomb, V. P., Jermiin, L. S., Patterson, D. J. & Sogin, M. L. 2002. Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia. Mol. Biol. Evol., 19:1782-1791.
36. Spahn, C. M. T., Beckmann, R., Eswar, N., Penczek, P. A., Sali, A., Blobel, G. & Frank, J. 2001. Structure of the 80S ribosome from Saccharomyces cerevisiae - tRNA-ribosome and subunit-subunit interactions. Cell, 107:373-386.
37. Stechmann, T. & Cavalier-Smith, T. 2002. Rooting the eukaryote tree by using a derived gene fusion. Science, 297:89-91.
38. Thompson, J. D., Higgins, D. G. & Gibson, T. J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22:4673-4680.
39. Travis, J. L. & Allen, R. D. 1981. Studies on the motility of the foraminifera. I. Ultrastructure of the reticulopodial network of Allogromia laticollaris (Arnold). J. Cell Biol., 90:211-221.
40. Van de Peer, Y., Nicolaï, S., De Rijk, P. & De Wachter, R. 1996. Database on the structure of small ribosomal subunit RNA. Nucl. Acids Res., 24:86-91.
41. Walter, A. E., Turner, D. H., Kim, J., Lyttle, M. H., Müller, P., Mathews, D. H., & Zuker, M. 1994. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Nat. Acad. Sci. USA, 91:9218-9222.
42. Warner, J. R. & Gorenstein, C. 1978. The ribosomal proteins of Saccharomyces cerevisiae. Meth. Cell Biol., 20:45-60.
43. Wimberly, B. T., Brodersen, D. E., Clemons, W. M. Jr., Morgan-Warren, R. J., Carter, A. P., Vonrhein, C., Hartsch T. & Ramakrishnan, V. 2000. Structure of the 30S ribosomal subunit. Nature, 407:327-339.
44. Wuyts, J., Van de Peer, Y. & De Wachter, R. 2001. Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucl. Acids Res., 29:5017-5028.
45. Wuyts, J., Van de Peer, Y., Winkelmans, T. & De Wachter, R. 2002. The European database on small subunit ribosomal RNA. Nucl. Acids Res., 30:183-185.
46. Zettler, L. A. A., Anderson, O. R. & Caron, D. A. 1999. Towards a molecular phylogeny of colonial spumellarian radiolaria. Mar. Micropaleontol., 36:67-79.
47. Zuker, M. & Jacobson, A. B. 1995. "Well-determined" regions in RNA secondary structure predictions. Application to small and large subunit rRNA. Nucl. Acids Res., 23:2791-2798.