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Evolution of Multicellular Animals As Deduced from 5S Rrna Sequences

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Evolution of Multicellular Animals As Deduced from 5S Rrna Sequences Volume 12 Number 12 1984 Nucleic Acids Research Evolution of muldcellular animals as deduced from 5S rRNA sequences: a possible early emergence of the Mesozoa Takeshi Ohama, Tsutomu Kumazaki, Hiroshi Hon and Syozo Osawa Laboratory of Molecular Genetics, Department of Biology, Faculty of Science, Nagoya University, Chikusa-ku, Nagoya 464, Japan Received 9 April 1984; Revised and Accepted 30 May 1984 ABSTRACT The nucleotide sequences of 5S rRNA from a mesozoan Dicyema rmisakiense and three metazoan species, i.e., an acorn-worm Saccoglossus kowaZlevskii, a moss-animal Bugula neritina, and an octopus Octopus vulgaris have been determined. A phylogenic tree of multicellular animals has been constructed from 73 5S rRNA sequences available at present including those from the above four sequences. The tree suggests that the mesozoan is the most ancient multicellular animal identified so far, its emergence time being almost the same as that of flagellated or ciliated protozoans. The branching points of planarians and nematodes are a little later than that of the mesozoan but are clearly earlier than other metazoan groups including sponges and jellyfishes. Many metazoan groups seem to have diverged within a relatively short period. INTRODUCTION The 5S rRNA is one of the molecules suited for studying the evolutionary process of widely separated organisms because of its universal occurrence with a low nucleotide substitution rate (1). To date, 69 5S rRNA sequences from 54 multicellular animals from almost all the major phyla have been determined (see ref. of (2)). However, the sequences from the Mesozoa, the Lophophorata and the Hemichordata have been wanting. We have therefore determined the 5S rRNA sequences from a mesozoan Dicyema misakiense (Phylum Mesozoa), a moss-animal BuguZa neritina (Phylum Lophophorata), an octopus Octopus vulgaris (Phylum Mollusca) and an acorn-worm Saccoglossus kowalevskii (Phylum Hemichordata). Using these sequences together with all multicellular aminal 5S rRNAs now available, we have constructed a phylogenic tree. MATERIALS AND METHODS BuguZa neritina and Octopus vulgaris were collected near the Sugashima Marine Biological Station, Nagoya University. Saccoglossus kowaZevskii was collected at the Woods Hole Marine Biological Laboratory, USA. For the isolation of Dicyema misakiense, about 120 gm of renal appendages were obtained from eight individuals of the octopus, Octopus vuZgaris, minced with scissors in two volumes of cold sea-water, shaken gently, and centrifuged for 5 min at 100 x g to sediment the bulk of the debris, leaving the mesozoans in © I R L Press Limited, Oxford, England. 5101 Nucleic Acids Research Dicyema G--UPLCA GGCCMCCACCCUGUCAGCCCCACGGPWAG Bugula GUCAACGCC N3JUCUCGGJCCAJCUAG Octopus CCC(JGU@IGA CUCCCGJ(VAG Saccoglossus GCCWGGCCACG IGCCCCG4AG CUGCG(JCGGCG3AGUACWGCAUGGGACCCGCCGrGGAiICfa(, GCnrAGGCUU Fig. 1. Nucleotide sequences of 5S rRNA from Dicyema misakiense (Mesozoa), Bugula neritina (moss-animal, Lophophorata), Octopus vulgaris (Mollusca) and Saccoglossus kowalevskii (acorn-worm, Hemichordata). the supernatant. The mesozoans were then sedimented by centrifugation for 10 min at 500 x g. The RNA was directly isolated by the phenol method (3) from the Octopus livers or whole organisms of the rest of the three species. The nucleotide sequence was determined by the chemical method of Peattie (4) and the enzy- matic method of Donis-Keller (5) using 3'- or 5'-labelled RNA. Certain parts of the sequence were confirmed by electrophoresis on a hot plate (6). A phylogenic tree was constructed by the average-linkage method (= WPGMA, see refs. 7, 8) and the UPGMA matrix method (8) using Knuc values that were calculated by the following equation (9, 7, 10) : Knuc = - (1/2) log [(1 - 2P - Q)(1 - 2Q)012], where Knuc is the evolutionary distance between two sequences compared, P and Q are the fractions of nucleotide sites showing transition- and transversion type differences, respectively. One gap vs. one nucleotide was counted as equal to one transversion-type substitution. RESULTS AND DISCUSSION SEQUENCE The 5S rRNA preparations from both Bugula and Octopus gave a clear single band on the gel and had 120 nucleotides, while those of Dicyema and Saccoglossus showed two bands. The Dicyema 5S rRNAs from the upper and lower bands consisted of 117 and 116 nucleotides, respectively, revealing no difference in sequence except that the upper RNA had an additional U at its 3'-terminus. The two Saccoglossus 5S rRNAs were both 120 nucleotides long, U at the 111th residue from the 5'-terminus of the upper RNA being replaced by C in the lower RNA. These sequences are shown in Fig. 1. SIMILARITY PERCENTS DISPLAY Fig. 2 shows a graphic display of simi- larity percents between the 5S rRNAs from human, an acorn-worm, a moss- animal, an octopus and a mesozoan Dicyema taken in ordinate and those from other animal species taken in abscissa. The 5S rRNAs from the former four species show rather high similarities (80-85%) to those from animals in most of the representative phyla, with exceptions of nematodes (symbols Jl-J3 in Fig. 2), fresh-water planarians (L2, L3) and a mesozoan (01). This suggests that the phyla to which these four species belong are related with most 5102 Nucleic Acids Research Cd co 0 to $~ 4-4..' H X J0. HU 100i H0 4-0 CU.0 c' c0 4-H v -H H : 0 P4 HD 4 O4-4 002i)0 0'0 OH_I > N CU > C0 1 0 -H , UC0 4-1m p -0-o0 0 0 $4 00cU'0 CU 14 M 41 C 0 CU e booo 0oC o CU N HC 0 -H1 0 CU o HCUO .CU CH 0 C J 4 O)00 -Hd * 444J 14CUS J0 04 HCU 02C4)0H00^2t, 0204.I (LI CO L) a0 f4 4 0 m4202 0 01 Q CUO0 02 -H 4-1 0 4-i 021 02 H .UCCU0a0 4H0 0') co 04S10to Q(4241NS O p U) 0 C 1 H 0 H 4. 14 02 LI) CU044 4 la 02144-JU4J 0 CCCU 0v 04-l.avoaH 0 0a01a 4 Ci 0 r- l co V co 0) ,~0vd CUCUC a4 C H4-CU-r-i H laCU-HZ Cd a 0 CU H *d ¢ fr~1402*-a 00CUX CU H H H C H14c42H14*CUr0 C 0CU O CUCU1o402 5103 Nucleic Acids Research 1V2 Knuc Fig. 3. Phylogenic tree of 5S rRNAs using 73 sequences from 54 multicellular animal and 11 protozoan sequences. Representative 50 species are displayed in the figure. The sequences from two or more species are identical or almost the same (e.g., human, rat, and bovine), only one of these species is shown. Also, usually only one out of two or more sequences in one species, if they exist, is shown. I---o--i : range of standard error of Knuc, ak (9). The following abbreviations are used for the species-name. [A] Vertebrata, Al : Homo sapiens (human), A2 : Cricetus cricetus (hamster), A3 : Iguana igu- ana (iguana), A4 : GaZZus gaZZus (hen), A5 : Xenopus Zaevis (toad), A6 : Not- ophthaZmus viridescens (newt). [B] Protochordata, Bl : HaZocynthia roretzi ascidian)**. [C] Echinodermata, Cl : Hemicentrotus puicherrimus (sea-urchin)* , C2 : Lytechinus variegatus (sea-urchin), C3 : Asterias vuZgaris (starfish)* 5104 Nucleic Acids Research C4 : Asterina pectinifera (starfish), C5 : Stichopus oshimae (sea-cucumber) *. [D] Hemichordata, Dl : Saccoglossus kowalevskii (acorn-worm)*. [E] Lopho- phorata, El : LinguZa anatina (lamp-shell), E2 : BuguZa neritina (moss-animal )*. [F] Sipunculoidea, Fl : Phascolopsis gouZdii (sipunculid-worm). [G] Arth- ropoda, Gl : Bombyx mori (silkworm), G2 : PhiZosamia cynthia (moth), G3 : DrosophiZa meZanogaster (fly), G4 : Acyrthosiphon magnoZiae (aphid), G5 : Ar- temia saZina (brine shrimp). [H] Annelida, Hl : Urechis unicinctus (spoon- worm)*, H2 : Perinereis brevicirris (sea-worm)*, H3 : SabeZZastarte japonica (sea-worm)*. [I] Mollusca, Il : Octopus vuZgaris (octopus)*, I2 : IZZex ille- cebrosus (squid), I3 : MytiZus eduZis (mussel), I4 : Arion rufus (snail), I5 : Helix pomatia (snail). [J] Aschelminthes, Jl : Caenorhabditis eZegans (ne- matode)**, J2 Caenorhabditis briggsae (nematode), J3 : Rhabditis tokai (ne- matode)*, J4 Brachionus pZicatiZis (rotifer)*. [K] Nemertinea, Kl : Lineus geniculatus (ribbon-worm)*, K2 : Emplectonema graciZe (ribbon-worm)*. [L] P1- atyhelminthes, Ll : PZanocera reticuZata (marine planarian)*, L2 & L3 : Duge- sia japonica Furuyu & Sanage (fresh-water planarians)*. [Ml Coelenterata, Ml : Spirocodon saltatrix (jellyfish)*, M2 : Chrysaora quinquecirrha (jellyfish) *, M3 : Nemopsis dofleini (jellyfish)*, M4 : AureZia aurita (jellyfish)**, M5 Anthopleura japonica (sea-anemone)*. [N] Porifera, Nl : Haliclona ocuZata (sponge), N2 : Hymeniacidon sanguinea (sponge), N3 : HaZichondria panicea (sponge). [0] Mesozoa, 01 : Dicyema misakiense*. [P] Protozoa, P1 : Crithidia fasciculata (trypanosome), P2 : Tetrahymena thermophila (ciliated protozoan) **, P3 : Euglena gracilis**. Symbols * and ** : the sequence determined in our laboratory and in our as well as other laboratories, respectively. metazoan phyla to almost an equal extent. The octopus sequence is close to a squid sequence (I2, ref. 11) as expected (90% identity). The sequence from the moss-animal is clearly similar to that of a lamp-shell LinguZa anatina (El, ref. 12), supporting the classical view that these two animals are related. The acorn-worm 5S rRNA shows higher similarities to those of the annelid species and the ribbon-worm species throughout (H1-H3, Kl-K2), than to those of the vertebrate species (Al-A6) and the ascidian species (Bl). This might mean that, in contrast to the anatomical evidence, the acorn-worm (the Hemichordata) is not particularly connected either to the vertebrates or the ascidian (the Protochordata), but rather to the annelid species. The mesozoan 5S rRNA (01, Dicyema) is the least similar not only to the sequences here reported but also to all of the metazoans and the protozoans so far sequenced (62-70%, see Fig. 2). Also notable is that the 5S rRNAs from the fresh-water planarians (L2, L3) and the nematodes (Jl-J3) are rela- tively less similar to the sequences of other multicellular animal groups (65 -70%) as previously emphasized (13, 14). These situations are shown by asteriscs with an arrow in Fig. 2. PHYLOGENIC TREE More detailed analyses have been made by constructing a phylogenic tree to deduce the sequence of appearance of the multicellular animals during evolution.
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