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Isolation of symbiotically expressed genes from the dinoflagellate symbiont of the solitary radiolarian Thalassicolla nucleata.

Associations between microbial symbionts and their hosts are fundamental trophic relationships that occur in both terrestrial and aquatic environments and depend upon regulated genomic communication between the interacting organisms. We are particularly interested in the photosymbiotic relationships that involve microscopic (protistan) algae in association with a variety of "invertebrate" hosts (protistan and metazoan); these relationships are fairly common in the marine environment and contribute significantly to nutrient flow in the nutrient-poor regions of the ocean where they occur. The symbiosis is essential to the survival of the host organisms, although the algal symbiont can exist in the free-living state.

Besides the conspicuous invertebrate photosymbioses that most people are familiar with (anemones and corals), a variety of protistan species also harbor cytoplasmic algal symbionts. Most notably, protozoa within the subphylum Sarcomastigophora (the foraminifera, radiolaria, and acantharia; collectively referred to as "sarcodine protozoa") exist in symbioses with a wide array of algae (Anderson, 1983; Lee and McEnery, 1983; Caron and Swanberg, 1990; Michaels, 1991). These sarcodine protozoa are often large for single-celled organisms. Solitary cells often attain sizes more than 1 mm in diameter (some benthic foraminifera form discs more than 1 cm in diameter), and the presence of complex pseuclopodial networks can increase the effective size of these organisms up to a few centimeters (Fig. 1). Some colonial species of radiolaria even form gelatinous pseudopodial matrices several centimeters in diameter and more than 1 m in length. These organisms are important contributors to the biological assemblages in all tropical and subtropical oceans of the world. Sarcodines form conspicuous zooplankton assemblages in oligotrophic surface waters, where they contribute significantly to primary productivity (by virtue of their intracellular symbionts), predation, and the vertical flux of organic material and crystal minerals, such as calcium carbonate and strontium sulfate (Caron and Swanberg, 1990; Swanberg and Caron, 1991; Caron et al., 1995; Michaels et al., 1995).

Our interest in the regulation of photosymbiotic relationships arose while working on the identification of the symbionts in planktonic foraminifera and radiolaria to determine whether co-evolution of host and symbiotic alga occurred (Gast and Caron, 1996; Gast et al., 2000). We molecularly identified several taxonomically different algae that form symbioses in the planktonic sarcodines. Dinofiagellates are the most common of these, but we also found prymnesiophyte and prasinophyte algae. Furthermore, it appears that most algal symbionts are actually genetically more similar to non-symbiotic algae than they are to other symbiotic algal lineages. This led us to wonder about what made very different algae suitable as symbionts, sometimes in the same host (Gast and Caron, 2001), and to hypothesize that symbiotic algae have something in common, which can be identified genetically, that makes them acceptable as symbionts. We have undertaken comparative studies of gene expression in a symbiotic alga to investigate the mechanisms of symbiotic communication.

We are studying the symbiont-host relationship between the dinoflagellate alga Scrippsiella nut ricula and the solitary planktonic radiolarian Thalassicolla nucleata. The radiolarian system allows us to compare the genes expressed in the symbiotic state of the algal symbiont with those expressed in the free-living state of the alga in culture. The information that we obtain from this system can be used to identify the genes necessary for maintaining the interaction, determine the timing of gene expression, examine the genomic characteristics associated with symbiotic-competence (why one alga is a good symbiont and another is not), and examine the mechanisms of secondary and higher level endosymbiotic events.

We chose to begin our work of isolating algal genes expressed in the symbiotic state by studying the dinoflagellate symbiont (Scrippsiella nutricula) of the solitary radiolarian T. nucleata (Fig. 1). To identify genes being expressed in the symbiosis, we required RNA from both the free-living and symbiotic states of the alga. We currently have the different algal symbionts as free-living laboratory cultures, but the intact association must be collected from the environment. T. nucleata generally harbors thousands of symbiotic algae, it can be collected from the environment fairly easily, and, most importantly, the host and symbiont can be separated from each other with minimal host RNA contamination of the sample. The host nucleus, organelles, and ribosomes are separated from the symbionts by the central capsule (pp. 90-94, Anderson, 1983). We believe that very little host mRNA will be present in the extracapsular material, and we are careful not to destroy the central capsule when stripping away the desired extracapsular matrix.

Thalassicolla nucleata was collected by plankton net tows in the Sargasso Sea and the San Pedro Channel. Individuals were transferred to sterile seawater in multiwell culture dishes and placed in lighted incubators or on workbenches at ambient temperatures. This allowed the hosts to clear themselves of prey items prior to recovery of the symbiont. All hosts were examined for prey before the extracapsular material was stripped away from the central capsule. Studies involving host incorporation of C (14) through the uptake of symbiont-produced photosynthate indicated that the interaction continued to function normally when the host was held in the laboratory (Anderson, 1978; Gast, unpubl. results). We believe that the symbiotic pattern of gene expression is also maintained. Stripped extracapsular material was immediately placed in RNALater (Ambion) until processed for RNA extraction (RNAqueous, Ambion). At least 200 individual hosts were collected and processed for each subtraction analysis.

Due to the relatively small amount of symbiotic-state RNA available for our project, we used a subtraction method that would permit the analysis of very small amounts of starting material. Through the use of two PCR enrichment amplifications, suppression subtractive hybridization (SSH; Diatchenko et al., 1996) allows as little as 25 ng of mRNA (or 50 ng of total RNA) to be analyzed. We used the Clontech PCR-Select cDNA Subtraction Kit to analyze both total RNA and mRNA from the dinoflagellate symbionts (Fig. 2). To date, we have completed five subtractions--one from total RNA that failed, three from total RNA that were successful but yielded mostly host and bacterial ribosomal genes, and one from mRNA that was successful. We switched to analyzing mRNA because we recovered as many ribosomal clones as symbiosis clones when we analyzed total RNA. Contaminating ribosomal fragments were not unexpected since they would not be removed by subtraction with cultured dinofiagellate RNA. We identified 23 clones as being potentially up-regulated in the symbiotic state of the alga.

Nucleotide Blast searches (Altschul et al., 1997) were conducted for sequences from each of the putatively upregulated clones that were isolated. Of the 23 selected clones, 8 turned out to be ribosomal genes from the host, bacteria, or fungi. Twelve of the remaining clones (C4 group) were very similar to each other, varying primarily by small differences in length. These clones had no significant sequence match in the database (Table 1). Of the remaining three clones, only F7 showed significant homology to database sequences. The homology between F7 and Cyplasin S is the result of three 30-base repeats in the clone sequence that are also present in the gene. This 30-base repeat seems to occur in other proteins as well, and may represent a shared structural region. There are generally very few algal or protist cDNA sequences in GenBank, so the overall lack of homology to sequences in the database is disappointing but not unexpected. We are continuing to screen clones from the final PCR products of our mRNA sub traction to obtain more genes unique to the symbiotic state of the alga.

Because of the small amount of RNA available from our symbiotic state, it was not possible to confirm differential gene expression using northern blot. Instead, we used cDNA generated from the free-living and symbiotic state RNAs in a dot blot format (Fig. 3). Clone F9 was included as a control for positive hybridization to the free-living cDNA. This and other clones represent potentially down-regulated genes in the symbiotic state of the alga. We have not begun to analyze these clone sequences, but we recognize that these are potentially informative as well. The dot blots allowed us to confirm that our differentially expressed clones were not expressed, or were expressed at a reduced level, in the free-living cDNA populations.

Suppression subtractive hybridization analysis generates fairly small cDNA fragments, so rapid amplification of cDNA ends (RACE) analyses must be used to obtain the full cDNA sequence. We began our RACE analysis with the B8 clone because we knew that we had the 3' end of the transcript. Currently we have about 800 basepairs of sequence for this clone. It has two open reading frames that are interrupted by a single stop codon in each. Neither of these reading frames has a start codon, and because the few dinofiagellate cDNAs that have been examined indicate the presence of fairly long 3' untranslated regions (300-500 basepairs), we may still not have reached the 5' end of the transcript. New primers are being designed to try and recover more of the 5' end. Our other clones are less defined as to whether they are at the 5' or 3' end of the cDNA, and we are currently extending from both ends.

In this decidedly ambitious project, we have been successful in recovering several genes that appear to be up-regulated in the symbiotic state of the dinofiagellate symbiont S. nutricula. We know of only one other study using SSH in a non-mammalian context. That study, on the sexual stages of diatoms (Armbrust, 1999), confirmed only 10 up-regulated clones, so our low number of recovered clones may not be unusual, especially since our RNA quantities were so limiting. We plan to acquire the full-length cDNA sequences for the clones we have; to pursue the construction of a cDNA library for the dinofiagellate symbiotic-state RNA; and to develop microarrays to aid in screening for differentially expressed genes.
Table 1

List of clones recovered and analyzed with suppression subtractive

Clone                                                Number of
group  BLASTn results                       E value   clones

C4     Human DNA clone RP11-100A16           0.049      12
F7     Aplysia punctata mRNA for Cyplasin    le-60       1
E7     Klebsiella pneumoniae SL032 plasmid   0.003       1
B8     Human chromosome 16 clone RP11-       0.095       1

Clone     Size of
group  fragment (bp)

C4          278
F7          161

E7          635
B8          367


We thank the anonymous reviewers of this manuscript for their helpful comments. This work was supported by the NASA Astrobiology Program through grant number NCC 2-1054 to the MBL Astrobiology Center. WHOI contribution number 10815.

Literature Cited

Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.

Anderson, O. R. 1978. Fine structure of a symbiont-bearing colonial radiolarian, Collosphaera globularis and 14C isotopic evidence for assimilation of organic substances from its zooxanthellae. J. Ultrastruct. Res. 62: 181-189.

Anderson, O. R. 1983. Radiolaria. Springer-Verlag, New York.

Armbrust, E. V. 1999. Identification of a new gene family expressed during the onset of sexual reproduction in the centric diatom Thalassiosira weissflogii. Appl. Environ. Microbiol. 65: 3121-3128.

Caron, D. A., and N. R. Swanberg. 1990. The ecology of planktonic sarcodines. Rev. Aquat. Sci. 3:147-180.

Caron, D. A., A. F. Michaels, N. R. Swanberg, and F. A. Howse. 1995. Primary productivity by symbiont-bearing planktonic sarcodines (Acantharia, Radiolaria, Foraminifera) in surface waters near Bermuda. J. Plankton Res. 17: 103-129.

Diatchenko, L., C. Y.-F. Lau, A. P. Campbell, A. Chenchik, F. Moqadam, B. Huang, S. Lukyanov, K. Lukyanov, N. Gurskaya, E. D. Sverdlov, and P. D. Siebert. 1996. Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. 93: 6025-6030.

Gast, R. J., and D. A. Caron. 1996. Molecular phylogeny of symbiotic dinoflagellates from Foraminifera and Radiolaria. Mol. Biol, Evol. 13:1192-1197.

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Gast, R. J., T. A. McDonnell, and D. A. Caron. 2000. srDNA-based taxonomic affinities of algal symbionts from a planktonic foraminifer and a solitary radiolarian. J. Phycol. 36: 172-177.

Lee, J. J., and M. E. McEnery. 1983. Symbiosis in foraminifera, Pp. 37-68 in Algal Symbiosis, E. L. Goff, ed. Cambridge University Press, Cambridge.

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Michaels, A. F., D. A. Caron, N. R. Swanberg, F. A. Howse, and C. M. Michnels. 1995. Planktonic sarcodines (Acantharia, Radiolaria, Foraminifera) in surface waters near Bermuda: abundance, biomass and vertical flux. J. Plankton Res. 17: 131-163.

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* To whom correspondence should be addressed. E-mail:

(1.) Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543

(2.) Marine Biological Laboratory, Woods Hole, Massachusetts 02543;

(3.) University of Southern California, Los Angeles, California 90089-0371

The paper was originally presented at a workshop titled Outcomes of Genome-Genome Interactions. The workshop, which was held at the J. Erik Jonsson Center at the National Academy of Sciences, Woods Hole, Massachusetts, from 1-3 May 2002, was sponsored by the Center for Advanced Studies in the Space Life Sciences at the Marine Biological Laboratory, and funded by the National Aeronautics and Space Administration under Cooperative Agreement NCC 2-1266.
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Author:Gast, Rebecca J.; Beaudoin, David J.; Caron, David A.
Publication:The Biological Bulletin
Geographic Code:1USA
Date:Apr 1, 2003
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