Accumulation pattern of amino acid substitutions in protein evolution

Summary A simple method for the evolutionary analysis of amino acid sequence data is presented and used to examine whether the number of variable sites (NVS) of a protein is constant during its evolution. The NVSs for hemoglobin and for mitochondrial cytochrome c are each found to be almost constant, and the ratio between the NVSs is close to the ratio between the unit evolutionary periods. This indicates that the substitution rate per variable site is almost uniform for these proteins, as the neutral theory claims. An advantage of the present analysis is that it can be done without knowledge of paleontological divergence times and can be extended to bacterial proteins such as bacterial c-type cytochromes. It is suggested that the NVS of cytochrome c has been almost constant even over the long period (ca. 3.0 billion years) of bacterial evolution but that at least two different substitution rates are necessary to describe the accumulated changes in the sequence. This two clock interpretation is consistent with fossil evidence for the appearance times of photosynthetic bacteria and eukaryotes.     

Structure of cDNA clones for the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from a fern (Asplenium cataractarum rosenstock,aspleniaceae), and its comparison with those of various seed plants

We isolated the small subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase (RuBisCO SSu) from a fern,Asplenium cataractarum and determined its 34 N-terminal amino acid sequence. We obtained a cDNA clone that contains the entire coding region of the SSu from the same fern species, using synthetic oligonucleotide probes derived from the above amino acid sequence. It contains a 525 bp open reading frame capable of coding for a polypeptide with 174 amino acids, 31 bp 5′-and 206 bp 3′-noncoding regions. It was also elucidated that the precursor to the SSu contains a transit peptide of 53 amino acid residues and a mature protein of 121 residues. We compared the deduced amino acid sequence of the fern SSu with those of 11 other vascular plant species (including gymnosperms, monocots and dicots). As low as 55% homology was observed between those of a fern and seed plants. Constancy of the amino acid substitution rate in RuBisCO SSu was supported by our relative rate test. Amino acid substitution rate per year per site for RuBisCO SSu was calculated to be 0.81×10⁻⁹ assuming that the separation between pteridophytes and seed plants arose 380 million years ago.     

Induction of Cytoplasmic Streaming and Movement of Chloroplast Induced by L-Histidine and its Derivatives in Leaves of Egeria densa

Rotational cytoplasmic streaming in leaves of Egeria densa wasinduced by light as well as by L-histidine (L-His). During bothtreatement with light and with L-His chloroplasts on the periclinalface were dislodged and moved to the anticlinal face where rotationalcytoplasmic streaming occurred. The effective concentrationof L-His was about 0.01 mM and the effect was almost saturatedat 0.1 mM. A derivative of L-His, 3-methyl-L-histidine, wasslightly less effective than L-His. By contrast, 1-methyl-L-histidinewas almost ineffective for induction of streaming, not onlyin Egeria but also in Vallisneria. Our resutlts are in markedcontrast to Fitting's result (1936) that 1-M-L-His is more effectivethan L-His. In Egeria, 1-methyl-L-His counteracted the stimulativeeffect of L-His. 1-Methyl-L-His penetrated into leaf cells ofEgeria to the same extent as 3-methyl-L-His and to a greaterextent than L-His. This observation excludes the possibilitythat the impermeability of leaves to 1-M-L-His might be responsiblefor its ineffectiveness. 1-M-L-His did not interfere with photodinesis.Differences in the mechanism of induction of rotational streamingby L-His and by light are discussed. ⁴ Present address: Fukui Institute of Technology, Gakuen, Fukui,910 Japan (Received July 16, 1990; Accepted December 20, 1990)     

HMG1-related DNA-binding protein isolated with V-(D)-J recombination signal probes.

In order to isolate cDNA clones for DNA-binding components of the V-(D)-J recombinase, phage libraries from a pre-B-cell line were screened with a radiolabeled probe containing recombination signal sequences (RSS). Among prospective clones, cDNA T160 was analyzed further. It produced a protein of 80.6 kDa which bound to DNA containing RSS but not to DNA in which the RSS had been mutated. A search of a data base revealed that the T160 protein has significant sequence homology (56%) to the nonhistone chromosomal protein HMG1 within the C-terminal region of 80 amino acids. DNA-binding analysis with truncated proteins showed that the HMG homology region is responsible for DNA binding. Using restriction fragment length polymorphisms, the T160 gene was mapped at the proximal end of mouse chromosome 2. Evidence was obtained for genetic linkage between the T160 gene and the recombination activator genes RAG-1 and RAG-2.     

Switch circular DNA formed in cytokine-treated mouse splenocytes: evidence for intramolecular DNA deletion in immunoglobulin class switching

We have characterized circular DNA in mouse splenocytes treated with the mitogen lipopolysaccharide (LPS) and various cytokines, including transforming growth factor beta (TGF-beta) and interleukin 4 (IL-4). Using probes of immunoglobulin heavy chain constant genes (CH), excision products of class switch recombination were identified. The majority of the clones contained the 3' portion of the switch mu (S mu) region and the 5' portion of other switch regions. Some clones contained 3'-S gamma sequences instead of 3'-S mu. This indicates that isotype switching may occur not only from C mu, but also from one of the C gamma genes to other CH genes further down-stream. In the presence of LPS, the cytokine TGF-beta enhanced the detection of 5'-S alpha-positive clones, while the lymphokine IL-4 enhanced 5'-S gamma 1 positives. The data support the notion that TGF-beta and IL-4 can direct isotype-specific class switching.     

Changes in the Subcellular Distribution of Free Amino Acids in Relation to Light Conditions in Cells of Chara corallina

Subcellular concentrations of free amino acids in internodal cells of a Characeae, Chara corallina, were measured in the dark and in the light. Using an intracellular perfusion technique, we measured concentrations of amino acids in the vacuole, in the flowing sol endoplasm and in the cortical gel layer. The sol endoplasm was predominantly the cytosol. On the basis of microscopic observations, the gel layer appeared to be occupied predominantly by a layer of chloroplasts, while the sol endoplasm was free from chloroplasts. Both in the light and in darkness, the major amino acids in the internodal cells were isoasparagine, glutamic acid, aspartic acid, serine, glycine and alanine, as reported by Sakano and Tazawa (1984). The same major amino acids are found in each of the three compartments. The pattern of distribution of amino acids in the vacuole was similar to that in the sol endoplasm, but quite different from that in the gel layer. The total level of amino acids in the light was lower than that in darkness. The amino acid composition did not change very much, but the subcellular distribution of amino acids differed significantly between cells subjected to illumination and those kept in the dark. Concentrations of amino acids in both the vacuole and the gel layer decreased, whereas those in the sol endoplasm were almost constant.     

Divergence pattern and selective mode in protein evolution: The example of vertebrate myoglobins and hemoglobin chains

Summary The evolutionary relation of vertebrate myoglobin and the hemoglobin chains including the agnathan hemoglobin chain is investigated on the basis of a new view of amino acid changes that is developed by canonical discriminant analysis of amino acid residues at individual sites. In contrast to the clear discrimination of amino acid residues between myoglobin, hemoglobin a chain, and hemoglobin chain in warm-blood vertebrates, the three types of globins in the lower class of vertebrates show so much variation that they are not well discriminated. This is seen particularly at the sites that are ascertained in mammals to carry the amino acid residues participating in stabilizing the monomeric structure in myoglobin and the residues forming the subunit contacts in hemoglobin. At these sites, agnathan hemoglobin chains are evaluated to be intermediate between the myoglobin and hemoglobin chains of gnathostomes. The variation in the phylogenetically lower class of globins is also seen in the internal region; there the amino acid residues of myoglobin and hemoglobin chains in the phylogenetically higher class exhibit an example of parallel evolution at the molecular level. New quantities, the distance of sequence property between discriminated groups and the variation within each group, are derived from the values of discriminant functions along the peptide chain, and this set of quantities simply describes an overall feature of globins such that the distinction between the three types of globins has been clearer as the vertebrates have evolved to become jawed, landed, and warm-blooded. This result strongly suggests that the functional constraint on the amino acid sequence of a protein is changed by living conditions and that severe conditions constitute a driving force that creates a distinctive protein from a less-constrained protein.Offprint requests to: J. Otsuka     

ALEXANDRIUM SATOANUM SP. NOV. (DINOPHYCEAE) FROM MATOYA BAY,CENTRAL JAPAN1

The gonyaulacoid dinofiagellate Alexandrium satoanum Yuki et Fukuyo sp. nov. is described from Matoya Bay, Pacific coast of central Japan. The species is distinctive in its conical epitheca with almost straight sides and dorsal concavity of the hypotheca. The plate formula is Po, pc, 4′, 6″, 6c, 10s, 5″″, and 2″″, including two accessory plates inside the sulcus. The apical pore plate is triangular and possesses an anterior attachment pore at the right margin. The first apical plate does not make contact with the apical pore plate and lacks a ventral pore. A posterior attachment pore lies at the center of the posterior sulcal plate. In Matoya Bay, vegetative cells occur as solitary cells or sometimes in pairs during late spring and early summer in low concentrations. In connection with this study, the following new combination is proposed: Alexandrium pseudogonyaulax (Biecheler) Horiguchi ex Yuki et Fukuyo comb. nov.