Amino Acid Composition and Terminal Sequences of Ferredoxins from Two Photosynthetic Green Bacteria

The amino acid composition of ferredoxins from Chlorobium thiosulfatophilum 8327 and Chloropseudomonas ethylicum, like C. thiosulfatophilum Tassajara, resembled ferredoxins from nonphotosynthetic anaerobes rather than Chromatium; the terminal sequences, however, more closely resembled Chromatium ferredoxin.     

基于编码序列、基因间序列和氨基酸序列构建的系统发生关系比较

以7种古菌、46种细菌和10种真核生物的基因组为样本,考虑碱基间的短程关联和长程关联作用,得到编码序列的密码对和基因间序列的三联体对中不同位点的二核苷酸频率,据此构建了基于编码序列和基因间序列的系统发生关系。无论是基于编码序列还是基因间序列对信息进行聚类,古菌或真核均被聚在一支上,表明聚类参数的选择是合适的;与基于氨基酸序列构建的系统发生关系进行两两比较,发现大部分硬壁菌的编码序列与基因间序列之间,以及编码序列与氨基酸序列之间的进化都存在较大差异。通过分析认为,只有综合考虑这三类序列的进化信息,才可能得到更自然的系统发生关系。     

Evolution of Chordate Actin Genes: Evidence from Genomic Organization and Amino Acid Sequences

The origin and evolutionary relationship of actin isoforms was investigated in chordates by isolating and characterizing two new ascidian cytoplasmic and muscle actin genes. The exon–intron organization and sequences of these genes were compared with those of other invertebrate and vertebrate actin genes. The gene HrCA1 encodes a cytoplasmic (nonmuscle)-type actin, whereas the MocuMA2 gene encodes an adult muscle-type actin. Our analysis of these genes showed that intron positions are conserved among the deuterostome actin genes. This suggests that actin gene families evolved from a single actin gene in the ancestral deuterostome. Sequence comparisons and molecular phylogenetic analyses also suggested a close relationship between the ascidian and vertebrate actin isoforms. It was also found that there are two distinct lineages of muscle actin isoforms in ascidians: the larval muscle and adult body-wall isoforms. The four muscle isoforms in vertebrates show a closer relationship to each other than to the ascidian muscle isoforms. Similarly, the two cytoplasmic isoforms in vertebrates show a closer relationship to each other than to the ascidian and echinoderm cytoplasmic isoforms. In contrast, the two types of ascidian muscle actin diverge from each other. The close relationship between the ascidian larval muscle actin and the vertebrate muscle isoforms was supported by both neighbor-joining and maximum parsimony analyses. These results suggest that the chordate ancestor had at least two muscle actin isoforms and that the vertebrate actin isoforms evolved after the separation of the vertebrates and urochordates. Received: 20 June 1996 / Accepted: 16 October 1996     

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids being exchanged. Recent developments have shown that models which allow for amino acid pairs to have independent rates of substitution offer improved fit over single rate models. However, these approaches have been limited by the necessity for large alignments in their estimation. An alternative approach is to assume that substitution rates between amino acid pairs can be subdivided into rate classes, dependent on the information content of the alignment. However, given the combinatorially large number of such models, an efficient model search strategy is needed. Here we develop a Genetic Algorithm (GA) method for the estimation of such models. A GA is used to assign amino acid substitution pairs to a series of rate classes, where is estimated from the alignment. Other parameters of the phylogenetic Markov model, including substitution rates, character frequencies and branch lengths are estimated using standard maximum likelihood optimization procedures. We apply the GA to empirical alignments and show improved model fit over existing models of codon evolution. Our results suggest that current models are poor approximations of protein evolution and thus gene and organism specific multi-rate models that incorporate amino acid substitution biases are preferred. We further anticipate that the clustering of amino acid substitution rates into classes will be biologically informative, such that genes with similar functions exhibit similar clustering, and hence this clustering will be useful for the evolutionary fingerprinting of genes.     

Alignment-free Comparison of Protein Sequences Based on Reduced Amino Acid Alphabets

Abstract

Protein sequences are treated as stochastic processes on the basis of a reduced amino acid alphabet of 10 types of amino acids. The realization of a stochastic process is described by associated transition probability matrix that corresponds to the process uniquely. Then new distances between transition probability matrices are defined for sequences similarity analysis. Two separate datasets are prepared and tested to identify the validity of the method. The results demonstrate the new method is powerful and efficient.     

Amino Acid Sequences of Porcine Fast and Slow Troponin T Isoforms

In this study, 10 troponin T isoforms from adult porcine skeletal muscle messenger RNA were clarified. These were eight fast- and two slow-type isoforms. Fast-type isoforms had three and two variable exons in the N-terminal and the C-terminal region respectively. Slow-type isoforms had one variable exon in the N-terminal region.     

Conservation of Amino Acid Sequences Between Human and Porcine Choline Acetyltransferase

Abstract: The amino acid sequence of 11 peptides generated from human placental choline acetyltransferase was compared to the corresponding amino acid sequences predicted from the nucleotide sequence of a recently cloned porcine choline acetyltransferase cDNA. These peptides, which were generated by cyanogen bromide cleavage or tryptic digestion, accounted for 23% of the amino acids in the enzyme. Of the 145 amino acids sequenced eight differed between the two species, yielding an identity of 94% over the regions sampled.
Of the eight amino acids that differed six could represent single base changes in the DNA sequence. These findings demonstrate strong sequence similarity between porcine and human choline acetyltransferase and indicate that they are closely related evolutionarily.     

Identification and Amino Acid Sequences of Tryptic Peptides of a Novel Ferredoxin-NADP+ Oxidoreductase from Rice

A 37-kDa protein purified from rice thylakoid membranes hasbeen identified as a ferredoxin-NADP⁺ oxidoreductase based onits catalysis of the reduction of nitro blue tetrazolium viaNADPH and its recognition by antibodies against ferredoxin-NADP⁺oxidoreductase. Amino acid sequences determined from trypticfragments of the enzyme further confirm the identity of theprotein and show the presence of unique sequences at the amino-terminus. (Received May 21, 1996; Accepted September 3, 1996)     

A New Method of Inference of Ancestral Nucleotide and Amino Acid Sequences

A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given the phylogeny and sequences of the extant species. A model of nucleotide or amino acid substitution was employed to analyze data of the present-day sequences, and maximum likelihood estimates of parameters such as branch lengths were used to compare the posterior probabilities of assignments of character states (nucleotides or amino acids) to interior nodes of the tree; the assignment having the highest probability was the best reconstruction at the site. The lysozyme c sequences of six mammals were analyzed by using the likelihood and parsimony methods. The new likelihood-based method was found to be superior to the parsimony method. The probability that the amino acids for all interior nodes at a site reconstructed by the new method are correct was calculated to be 0.91, 0.86, and 0.73 for all, variable, and parsimony-informative sites, respectively, whereas the corresponding probabilities for the parsimony method were 0.84, 0.76, and 0.51, respectively. The probability that an amino acid in an ancestral sequence is correctly reconstructed by the likelihood analysis ranged from 91.3 to 98.7% for the four ancestral sequences.     

Complete Amino Acid Sequences of Three Proteinase Inhibitors from White Sword Bean (Canavalia gladiata)

Three major serine proteinase inhibitors (SBI-1, -2, and -3) were purified from the seeds of white sword bean (Canavalia gladiata) by FPLC and reversed-phase HPLC. The sequences of these inhibitors were established by automatic Edman degradation and TOF-mass spectrometry. SBI-1, -2, and -3 consisted of 72, 73, and 75 amino acid residues, with molecular masses of 7806.5, 7919.8, and 8163.4, respectively. The sequences of SBI-1 and -2 coincided with those of CLT I and II [Terada et al. (1994) Biosci. Biotech. Biochem., 58, 376-379] except only N- or C-terminal amino acid residues. Analysis of the amino acid sequences showed that the active sites of the inhibitors contained a Lys²¹-Ser²² against trypsin and Leu⁴⁸-Ser⁴⁹ against chymotrypsin, respectively. Further, it became apparent that about seven disulfide bonds were present. These results suggest that sword bean inhibitors are members of the Bowman-Birk proteinase inhibitor family.     

The Origin of Chlorarachniophyte Plastids, as Inferred from Phylogenetic Comparisons of Amino Acid Sequences of EF-Tu

A molecular phylogenetic analysis of elongation factor Tu (EF-Tu) proteins from plastids was performed in an attempt to identify the origin of chlorarachniophyte plastids, which are considered to have evolved from the endosymbiont of a photosynthetic eukaryote. Partial sequences of the genes for plastid EF-Tu proteins (1,080–1,089 bp) were determined for three algae that contain chlorophyll b, namely, Gymnochlora stellata (Chlorarachniophyceae), Bryopsis maxima (Ulvophyceae), and Pyramimonas disomata (Prasinophyceae). The deduced amino acid sequences were used to construct phylogenetic trees of the plastid and bacterial EF-Tu proteins by the maximum likelihood, the maximum parsimony, and the neighbor joining methods. The trees obtained in the present analysis suggest that all plastids that contain chlorophyll b are monophyletic and that the chlorarachniophyte plastids are closely related to those of the Ulvophyceae. The phylogenetic trees also suggest that euglenophyte plastids are closely related to prasinophycean plastids. The results indicate that the chlorarachniophyte plastids evolved from a green algal endosymbiont that was closely related to the Ulvophyceae and that at least two secondary endosymbiotic events have occurred in the lineage of algae with plastids that contain chlorophyll b. Received: 10 March 1997 / Accepted: 28 July 1997     

Isolation and Amino Acid Sequences of Small Tryptic Peptides from the Oxidized Ala Chain of Ricin D

Twelve tryptic peptides as well as free arginine were isolated from the performic acid-oxidized Ala chain of ricin D by gel filtration on Sephadex G–25 and Dowex 1×2 column chromatography followed by paper chromatography. Total number of the amino acid residues in these peptides accounted for 90 out of 263 residues in the Ala chain of ricin D.

The amino acid sequences of nine peptides were determined by manual Edman degradation.     

Ammo-Terminal Amino Acid Sequences of Pea Phytochrome II Fragments Obtained by Limited Proteolysis

Apical shoot of pea seedling contains two immunochemically distinctspecies of phytochrome, type I (PI) and type II (PII) [Abe etal. (1985) Plant Cell Physiol. 26: 1387-1399]. A PII samplewas prepared from crude extracts from apical shoot of 7-day-old,light-grown pea (Pisum sativum L. cv. Alaska) seedlings, usingbrushite, DEAE-agarose and an agarose linked monoclonal anti-peaPII antibody (mAPll) column chromatography. More than 75% ofthe PII sample consisted of one major 115 kDa chromopeptide,and less than 25% of PII was composed of two minor non-chromophoric49 and 48 kDa fragments, as judged by SDS-polyacrylamide gelelectrophoresis and zinc-induced chromophore fluorescence analysis.Limited proteolysis of PII was performed with either trypsinor Staphylococcus aureus V8 protease, and the resulting fragmentswere separated by SDS-polyacrylamide gel electrophoresis andblotted electrophoretically onto a polyvinylidene difluoridemembrane. Amino-terminal amino acid sequences of the four fragmentsof PII cut from the membrane were determined by a gas-phasesequencer. The sequence of the determined regions (76 aminoacid residues in total), reveals that PII was 63% homologouswith PI. Hence the primary structure of PII is distinct fromthat of PI. (Received July 21, 1989; Accepted September 1, 1989)     

Rice Embryo Globulins: Amino-Terminal Amino Acid Sequences, cDNA Cloning and Expression

A globulin fraction prepared from rice embryos contained polypeptidesor polypeptide groups of 49 kDa (designated REG1), 46 kDa (designatedREG2), about 35 kDa, 32 kDa and 25 kDa. The amino-terminal sequencesof REG1 and the major polypeptide in the 35-kDa group were identical,suggesting that the REG1 polypeptide undergoes partial proteolyticprocessing that removes a carboxy-terminal region. A cDNA clone,designated pcREG2, encoding REG2 was isolated, and its nucleotidesequence was determined. The deduced amino acid sequence ofREG2 was found to be 68% identical to that of the maize GLB2globulin. Reg2 mRNA was present at high levels during embryodevelopment for up to 14 days after flowering (DAF). Lower levelswere found 20 DAF when the maturation of embryos was almostcompleted, and at the dry mature stage. Reg2 mRNA almost disappearedupon imbibition of isolated dry mature embryos but it was re-inducedat a low level by further treatment with ABA. The expressionof Reg2 was not induced by ABA in suspension-cultured cells,unlike that of Osem, one of the late embryogenesis abundantprotein (LEA) genes. (Received November 6, 1995; Accepted April 22, 1996)     

The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree

To aid in future efforts to accurately reconstruct the vertebrate tree, a quantitative measure of phylogenetic informativeness was applied to nucleotide and amino acid sequences for a set of 11 genes. We identified orthologues and assembled published fossil-calibrated divergence times between taxa that had been sequenced for each gene. Rates of molecular evolution for each site were estimated to characterize the molecular evolutionary pattern of genes and to calculate the phylogenetic informativeness. The fast-evolving gene albumin yielded the highest informativeness over the period from 60 million years ago to 500 million years ago. In contrast, calmodulin yielded the lowest informativeness, presumably because functional constraint minimized substitutions in the amino acid sequence. The gene c-myc showed an intermediate level of informativeness. The nucleotide sequence of cytochrome b showed extremely high utility for recent epochs, but low utility for times before 100 million years ago. We ranked nine other genes for their utility during the epochs of the divergence of the muroid rodents, early placental mammals, early vertebrates, and early metazoa, yielding results consistent with, but more precise than, previous studies. Interestingly, DNA sequence always exceeded amino acid sequence in informativeness over all time scales, yet support values were at best moderately higher. For epochs not subject to strong phylogenetic conflict due to convergence, we advocate gleaning the additional power of the threefold increase in number of characters that is present for DNA sequences over resorting to the less noisy but less informative amino acid sequences.     

Chloroplast and Cytosol Isozymes of Cu,Zn-Superoxide Dismutase: Their Characteristic Amino Acid Sequences

lsozymes of CuZn-superoxide dismutase (SOD) were purified from angiosperms (spinach and rice), fern (horsetail) and green alga (Spirogyra). Occurrence of CuZn-SOD was confirmed by its purification in the group of green algae which shows the phragmoplast type of cell division. Purified CuZn-SODS are divided to chloroplast and cytosol types by their cellular localization and immunological properties. Their amino acid compositions, absorption spectra, CD spectra, and sensitivity to hydrogen peroxide also are distinguished from each other. All organisms including Spirogyra contain both types of isozyme. Thus, the divergence of the two types of CuZn-SOD isozyme occurred immediately after its acquisition by the most evolved green algae.

Amino acid sequences of amino-terminal regions of CuZn-SOD isozyrnes from spinach, rice and horsetail were determined and compared with those of CuZn-SODS from other plants. The chloroplast and cytosol isozymes of CuZn-SOD show each characteristic sequences. Sequence differences among the cytosol CuZn-SODS are greater than those among the chloroplast CuZn-SODS. These observations indicate that each type of isozyme had independently evolved after the acquisition of CuZn-SOD.     

The Lectins of Sophora japonica: I. Purification Properties and N-Terminal Amino Acid Sequences of Two Lectins from Leaves

Two lectins, Leaf Lectin I and Leaf Lectin II (LLI and LLII) were purified from the leaves of Sophora japonica. Like the Sophora seed lectin, LLI and LLII are tetrameric glycoproteins containing a single subunit with respect to size. The subunits of LLI (32 kilodaltons) and LLII (34 kilodaltons) are slightly larger than those of the seed lectin (29.5 kilodaltons). The three Sophora lectins display indistinguishable specificities, amino acid compositions, specific hemagglutinin activities, and extinction coefficients. Although very closely related to the seed lectin, the leaf and seed lectins are not immunologically identical and they differ in subunit molecular weights, carbohydrate content, and in the pH sensitivity of their hemagglutinin activities. N-terminal amino acid sequence analysis shows that although they are homologous proteins, the three Sophora lectins are products of distinct genes.