双序列比对基础和应用实例

首先介绍序列比对的分子生物学基础,即核酸序列基本单元核苷酸和蛋白质序列基本单元氨基酸。文中以精心设计的图表列出四种核苷酸和二十种氨基酸的名称、性质和分类。第2节简述序列比对基础,包括相似性和同源性基本概念、整体比对和局部比对、点阵图方法、动态规划和启发式算法、计分矩阵和空位罚分,以及常用软件和分析平台。第3节介绍核酸序列比对中常用计分矩阵DNAfull,蛋白质序列比对中常用计分矩阵BLOSUM62和PAM250。第4-8节则以血红蛋白、多肽毒素、植物转录因子、癌胚抗原和唾液酸酶为例,介绍双序列比对的具体应用。通过这些实例,说明如何选择分析平台和比对程序、如何设置计分矩阵和空位罚分,如何分析比对结果及其生物学意义。文末进行简要总结。     

The α-gliadin gene family. II. DNA and protein sequence variation, subfamily structure, and origins of pseudogenes

 The derived amino-acid sequences of all reported α-gliadin clones are compared and analyzed, and the patterns of sequence change within the α-gliadin family are examined. The most variable sequences are two polyglutamine domains. These two domains are characteristic features of the α-gliadin storage proteins and account for most of the variation in protein size of this otherwise highly conserved protein family. In addition, their encoding DNA sequences form microsatellites. Single-base substitutions in the α-gliadin genes show a preponderance of transitions, including the C to T substitution which contributes to the generation of stop codons, and consequently to the observation that approximately 50% of the α-gliadin genes are pseudogenes. In one unusual gene, a microsatellite has expanded to 321 bp as compared to the normal 36–72 bp, and may result from similar mechanisms that produce polyglutamine-associated genetic diseases in humans. A comparison of the 27 reported sequences show several α-gliadin gene subfamilies, at least some of which are genome specific. Received: 1 October 1996/Accepted: 20 December 1996     

Progressive sequence alignment and molecular evolution of the Zn-containing alcohol dehydrogenase family

Summary Sequences of 47 members of the Zn-containing alcohol dehydrogenase (ADH) family were aligned progressively, and an evolutionary tree with detailed branch order and branch lengths was produced. The alignment shows that only 9 amino acid residues (of 374 in the horse liver ADH sequence) are conserved in this family; these include eight Gly and one Val with structural roles. Three residues that bind the catalytic Zn and modulate its electrostatic environment are conserved in 45 members. Asp 223, which determines specificity for NAD, is found in all but the two NADP-dependent enzymes, which have Gly or Ala. Ser or Thr 48, which makes a hydrogen bond to the substrate, is present in 46 members. The four Cys ligands for the structural zinc are conserved except in -crystallin, the sorbitol dehydrogenases, and two bacterial enzymes. Analysis of the evolutionary tree gives estimates of the times of divergence for different animal ADHs. The human class II () and class III () ADHs probably diverged about 630 million years ago, and the newly identified human ADH6 appeared about 520 million years ago, implying that these classes of enzymes may exist or have existed in all vertebrates. The human class I ADH isoenzymes (, , and ) diverged about 80 million years ago, suggesting that these isoenzymes may exist or have existed in all primates. Analysis of branch lengths shows that these plant ADHs are more conserved than the animal ones and that class III ADHs are more conserved than class I ADHs. The rate of acceptance of point mutations (PAM units) shows that selection pressure has existed for ADHs, implying that these enzymes play definite metabolic roles.Offprint requests to: B.V. Plapp     

Characterization of frequencies and distribution of single nucleotide insertions/deletions in the human genome

Most of the studies on single nucleotide variations are on substitutions rather than insertions/deletions. In this study, we examined the distribution and characteristics of single nucleotide insertions/deletions (SNindels), using data available from dbSNP for all the human chromosomes. There are almost 300,000 SNindels in the database, of which only 0.8% are validated. They occur at the frequency of 0.887 per 10 kb on average for the whole genome, or approximately 1 for every 11,274 bp. More than half occur in regions with mononucleotide repeats the longest of which is 47 bases. Overall the mononucleotide repeats involving C and G are much shorter than those for A and T. About 12% are surrounded by palindromes. There is general correlation between chromosome size and total number for each chromosome. Inter-chromosomal variation in density ranges from 0.6 to 21.7 per kilobase. The overall spectrum shows very high proportion of SNindel of types -/A and -/T at over 81%. The proportion of -/A and -/T SNindels for each chromosome is correlated to its AT content. Less than half of the SNindels are within or near known genes and even fewer (<0.183%) in coding regions, and more than 1.4% of -/C and -/G are in coding compared to 0.2% for -/A and -/T types. SNindels of -/A and -/T types make up 80% of those found within untranslated regions but less than 40% of those within coding regions. A separate analysis using the subset of 2324 validated SNindels showed slightly less AT bias of 74%, SNindels not within mononucleotide repeats showed even less AT bias at 58%. Density of validated SNindels is 0.007/10 kb overall and 90% are found within or near genes. Among all chromosomes, Y has the lowest numbers and densities for all SNindels, validated SNindels, and SNindels not within repeats.     

Definition of the tempo of sequence diversity across an alignment and automatic identification of sequence motifs: Application to protein homologous families and superfamilies

It is often possible to identify sequence motifs that characterize a protein family in terms of its fold and/or function from aligned protein sequences. Such motifs can be used to search for new family members. Partitioning of sequence alignments into regions of similar amino acid variability is usually done by hand. Here, I present a completely automatic method for this purpose: one that is guaranteed to produce globally optimal solutions at all levels of partition granularity. The method is used to compare the tempo of sequence diversity across reliable three-dimensional (3D) structure-based alignments of 209 protein families (HOMSTRAD) and that for 69 superfamilies (CAMPASS). (The mean alignment length for HOMSTRAD and CAMPASS are very similar.) Surprisingly, the optimal segmentation distributions for the closely related proteins and distantly related ones are found to be very similar. Also, optimal segmentation identifies an unusual protein superfamily. Finally, protein 3D structure clues from the tempo of sequence diversity across alignments are examined. The method is general, and could be applied to any area of comparative biological sequence and 3D structure analysis where the constraint of the inherent linear organization of the data imposes an ordering on the set of objects to be clustered.     

Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility

In comparative modeling, the quality of amino acid sequence alignment still constitutes a major bottleneck in the generation of high quality models of protein three-dimensional (3D) structures. Substantial efforts have been made to improve alignment quality by revising the substitution matrix, introducing multiple sequences, replacing dynamic programming with hidden Markov models, and incorporating 3D structure information. Improvements in the gap penalty have not been a major focus, however, following the development of the affine gap penalty and of the secondary structure dependent gap penalty. We revisited the correlation between protein 3D structure and gap location in a large protein 3D structure data set, and found that the frequency of gap locations approximated to an exponential function of the solvent accessibility of the inserted residues. The nonlinearity of the gap frequency as a function of accessibility corresponded well to the relationship between residue mutation pattern and residue accessibility. By introducing this relationship into the gap penalty calculation for pairwise alignment between template and target amino acid sequences, we were able to obtain a sequence alignment much closer to the structural alignment. The quality of the alignments was substantially improved on a pair of sequences with identity in the "twilight zone" between 20 and 40%. The relocation of gaps by our new method made a significant improvement in comparative modeling, exemplified here by the Bacillus subtilis yitF protein. The method was implemented in a computer program, ALAdeGAP (ALignment with Accessibility dependent GAp Penalty), which is available at http://cib.cf.ocha.ac.jp/target_protein/.     

Structure-based sequence alignment of elongation factors Tu and G with related GTPases involved in translation

The G domain and domain II in the crystal structure of Thermus thermophilus elongation factor G (EF-G) were compared with the homologous domains in Thermus aquaticus elongation factor Tu (EF-Tu). Sequence alignment derived from the structural superposition was used to define conserved sequence elements in domain II. These elements and previously known conserved sequence elements in the G domain were used to guide the alignment of the sequences of Sulfolobus acidocaldarius elongation factor 2, human elongation factor 2, and Escherichia coli initiation factor 2 and release factor 3 to the aligned sequences of EF-G and EF-Tu. This alignment, which deviates from previously published alignments, has evolutionary implications and leads to alternative interpretations of biochemical data concerning the interaction of elongation factors with the -sarcin/ricin region of the ribosome. A single conserved sequence motif in domain II was identified and used to further characterize the GTPase subfamily of translation factors and related proteins. It was shown that the motif is found in most if not all the members of the family. Apparently, the common characteristic of these GTPases is an extensive consensus structural unit that possibly accounts for a similar interaction with the ribosome and is composed of two domains homologous to the G domain and domain II in EF-Tu and EF-G.     

A method for detecting distant evolutionary relationships between protein or nucleic acid sequences in the presence of deletions or insertions

Summary A method for detecting homology between two protein or nucleic acid sequences which require insertions or deletions for optimum alignment has been devised for use with a computer. Sequences are assessed for possible relationship by Monte Carlo methods involving comparisons between the alignment of the real sequences and alignments of randomly scrambled sequences of the Same composition as the real sequences, each alignment having the optimum number of gaps. As each gap is successively introduced into a comparison (real or random) a maximum score is determined from the similarity of the aligned residues. From the distribution of the maximum alignment scores of randomly scrambled sequences having the same number of gaps, the percentage of random comparisons having higher scores is determined, and the smallest of these percentage levels for each pair of sequences (real or random) indicates the optimum alignment. The fraction of the comparisons of random sequences having percentage levels at their optimum alignment below that of the real sequence comparison at its optimum estimates the probability that such an alignment might have arisen by chance. Related sequences are detected since their optimum alignment score, by virtue of a contribution from ancestral homology in addition to optimised random considerations, occupies a more extreme position in the appropriate frequency distribution of scores than do the majority of optimum scores of randomly scrambled sequences in their appropriate distributions.Application of this optimum match method of sequence comparison shows that the sensitivity of the maximum match method of Needleman and Wunsch (1970) decreases quite dramatically with sequence comparisons which require only a few gaps for a reasonable alignment, or when sequences differ greatly in length. The maximum match method as applied by Barker and Dayhoff (1972) has the additional disadvantage that deletions which have occurred in the longer of two homologous protein sequences further decrease the sensitivity of detection of relationship. The constrained match method of Sankoff and Cedergren (1973) is seen to be misleading since large increments in the alignment score from added gaps do not necessarily result in a high total alignment score required to demonstrate sequence homology.     

On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles

Structural alignments often reveal relationships between proteins that cannot be detected using sequence alignment alone. However, profile search methods based entirely on structural alignments alone have not been found to be effective in finding remote homologs. Here, we explore the role of structural information in remote homolog detection and sequence alignment. To this end, we develop a series of hybrid multidimensional alignment profiles that combine sequence, secondary and tertiary structure information into hybrid profiles. Sequence-based profiles are profiles whose position-specific scoring matrix is derived from sequence alignment alone; structure-based profiles are those derived from multiple structure alignments. We compare pure sequence-based profiles to pure structure-based profiles, as well as to hybrid profiles that use combined sequence-and-structure-based profiles, where sequence-based profiles are used in loop/motif regions and structural information is used in core structural regions. All of the hybrid methods offer significant improvement over simple profile-to-profile alignment. We demonstrate that both sequence-based and structure-based profiles contribute to remote homology detection and alignment accuracy, and that each contains some unique information. We discuss the implications of these results for further improvements in amino acid sequence and structural analysis.     

Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments

To understand how protein segments are inserted and deleted during divergent evolution, a set of pairwise alignments contained exactly one gap, and therefore arising from the first insertion-deletion (indel) event in the time separating the homologs, was examined. The alignments showed that "structure breaking" amino acids (PGDNS) were preferred within and flanking gapped regions, as are two residues with hydrophilic side-chains (QE) that frequently occur at the surface of protein folds. Conversely, hydrophobic residues (FMILYVW) occur infrequently within and flanking the gapped region. These preferences are modestly different in protein pairs separated by an episode of adaptive evolution, than in pairs diverging under strong functional constraints. Surprisingly, regions near an indel have not evolved more rapidly than the sequence pair overall, showing no evidence that an indel event must be compensated by local amino acid replacement. The gap-lengths are best approximated by a Zipfian distribution, with the probability of a gap of length L decreasing as a function of L(-1.8). These features are largely independent of the length of the gap and the extent of divergence (measured by both silent and non-silent sequence changes) separating the two proteins. Surprisingly, amino acid repeats were discovered in more than a third of the polypeptide segments in and around the gap. These correspond to repeats in the DNA sequence. This suggests that a signature of the mechanism by which indels occur in the DNA sequence remains in the encoded protein sequences. These data suggest specific tools to score gap placement in an alignment. They also suggest tools that distinguish true indels from gaps created by mistaken gene finding, including under-predicted and over-predicted introns. By providing mechanisms to identify errors, the tools will enhance the value of genome sequence databases in support of integrated paleogenomics strategies used to extract functional information in a post-genomic environment.     

Effects of gap size and associated changes in light and soil moisture on the understorey vegetation of a Hungarian beech forest

In European beech forests windstorms often create canopy gaps and change the level of incident light, soil moisture and nutrient availability on the forest floor. Understanding the interrelations between gap size and environmental change, and the effects these have on regeneration processes is a prerequisite for developing techniques of nature-based forestry. The aims of this study were to investigate the effects of gap size on the resulting spatial distributions of key abiotic environmental variables (light and soil moisture) in gaps, and to study how light and soil moisture affect the abundance and distribution of herb layer species. To do this we used eight artificially created gaps – three large (diameter: 35–40 m) and five small (diameter: 10–15 m) – in a mesotrophic submontane beech forest. Data on species’ importance and substrate types were collected in systematically distributed 1 m×1 m quadrats before gap creation and on four occasions during the next two growing seasons. Hemispherical photographs were taken and analysed to estimate relative light intensity. Soil moisture was measured by frequency domain and capacitance probes. It was found that gap size had a profound effect on the environmental variables measured. While relative light intensity values in small gaps did not reach those in large gaps, soil moisture levels did reach similar maximum values in gap centres regardless of gap size. Richness, composition and total cover of herbaceous vegetation were different in small versus large gaps. Much of this difference was attributed to the presence of specific relative light intensities and also to the increased amount of available soil moisture in gaps. Species were differently affected by the combined effects of light and soil moisture, as well as by differences in available substrates. All this resulted in species-specific distribution patterns within gaps.     

The alignment of sets of sequences and the construction of phyletic trees: An integrated method

Summary In this paper we argue that the alignment of sets of sequences and the construction of phyletic trees cannot be treated separately. The concept of good alignment is meaningless without reference to a phyletic tree, and the construction of phyletic trees presupposes alignment of the sequences.We propose an integrated method that generates both an alignment of a set of sequences and a phyletic tree. In this method a putative tree is used to align the sequences and the alignment obtained is used to adjust the tree; this process is iterated. As a demonstration we apply the method to the analysis of the evolution of 5S rRNA sequences in prokaryotes.     

The effects of gap disturbance on the seedling emergence,survival and growth of two different native species in Inner Mongolia

A field study was conducted to investigate the effects of gap disturbance on the seedling establishment process of two native species. Seeds of Agropyron cristatum and Stipa krylovii were reseeded to artificially created gaps in a degraded steppe in North China. There were seven treatments: shoot gaps and root gaps (10 cm, 20 cm and 40 cm in diameters), no gaps (control). Shoot gaps were formed by removing above ground vegetation and below ground biomass without restricting the re-growth of neighbor roots back into the gap. The root gaps were accomplished by using polyvinyl chloride pipes sunk in the soil of shoot gaps to exclude neighboring roots. Seedling emergence, survival and growth performance after 90 days of growing were recorded for both species. Gap significantly increased soil moisture, especially for root gaps. Emergence increased significantly for both species as gap size increased. Seedling emergence and survivorship of both species were greater in gaps than in controls. However, the gap size showed a significantly negative effect on Agropyron cristatum's survivorship. Growth performance of Agropyron cristatum and Stipa krylovii differ in their response to gap disturbance. Gap had positive effects on seedling growth (including seedling height, dry weight, and numbers of tillers and leaves) of Stipa krylovii, but had negative effects on seedling growth of Agropyron cristatum. The two species have significantly different responses to gap disturbance. All results suggest that Stipa krylovii is a gap-enhanced species, and Agropyron cristatum is not. Predation by insects may be one of the key reasons to explain the stand dominance in this grassland.     

The effect of seed mass and gap size on seed fate of tropical rain forest tree species in guyana

Abstract: For eleven tree species, differing in seed mass, germination success (emergence success for two small-seeded species) and the causes of failure to germinate were studied in the forest understorey and in logging gaps in the tropical rain forests of Guyana. In the forest understorey, germination success increased with seed mass. However, as gap size increased the difference between smaller and larger seeded species diminished because germination success of smaller-seeded species increased slightly, while that of larger-seeded species decreased dramatically. The negative effect of gap size on germination success of larger-seeded species was caused by an increased risk of desiccation with gap size, which was a far more important seed mortality agent for larger than for smaller-seeded species. Generally, seeds of smaller-seeded species suffered more from insect predation and were removed at higher rates than larger-seeded species. On the other hand, larger-seeded species were eaten more by mammals than smaller-seeded species. It is concluded that logging can result in shifts in the species composition in the tropical rain forests of Guyana which are dominated by species with large seeds, since germination success of larger-seeded species is dramatically reduced in large logging gaps.     

Immunochemical characterization of the gap junction protein connexin45 in mouse kidney and transfected human HeLa cells

Antibodies to the gap junction protein connexin45 (Cx45) were obtained by immunizing rabbits with fusion protein consisting of glutathione S-transferase and 138 carboxy-terminal amino acids of mouse Cx45. As shown by immunoblotting and immunofluorescence, the affinity-purified antibodies recognized Cx45 protein in transfected human HeLa cells as well as in the kidney-derived human and hamster cell lines 293 and BHK21, respectively. In Cx45-transfected HeLa cells, this protein is phosphorylated as demonstrated by immunoprecipitation after metabolic labeling. The phosphate label could be removed by treatment with alkaline phosphatase. A weak phosphorylation of Cx45 protein was also detected in the cell lines 293 and BHK21. Treatment with dibutyryl cyclic adenosine or guanosine monophosphate (cAMP, cGMP) did not alter the level of Cx45 phosphorylation, in either Cx45 transfectants or in 293 or BHK21 cells. The addition of the tumor-promoting agent phorbol 12-myristate 13-acetate (TPA) led to an increased ³²P phosphate incorporation into the Cx45 protein in transfected cells.The Cx45 protein was found in homogenates of embryonic brain, kidney, and skin, as well as of adult lung. In kidney of four-day-old mice, Cx45 was detected in glomeruli and distal tubules, whereas connexin32 and –26 were coexpressed in proximal tubules. No connexin43 protein was detected in renal tubules and glomeruli at this stage of development. Our results suggest that cells in proximal and distal tubules are interconnected by gap junction channels made of different connexin proteins. The Cx45 antibodies characterized in this paper should be useful for investigations of Cx45 in renal gap junctional communication.     

Amino acid sequence of human factor D of the complement system: Similarity in sequence between factor D and proteases of non-plasma origin

The amino acid sequence of human factor D is proposed from the analysis of the peptides produced by treatment of the factor D with cyanogen bromide, iodosobenzoic acid, trypsin and V-8 protease. Comparison of the proposed sequence with the sequences of other serine esterases indicated that factor D, although it is a plasma serine esterase, is more closely related to certain proteases not found in the plasma than to other plasma serine esterases of the complement system. For example, 36% and 32% identity in amino acid sequence was found on comparison of factor D with elastase and group-specific protease, respectively. Whereas only 27% and 18% identity was observed between factor D and the other complement serine esterases, Clr and factor B, respectively.     

Cyclic AMP induces rapid increases in gap junction permeability and changes in the cellular distribution of connexin43

The rapid effects of cAMP on gap junction-mediated intercellular communication were examined in several cell types which express different levels of the gap junction protein, connexin43 (Cx43), including immortalized rat hepatocyte and granulosa cells, bovine coronary venular endothelial cells, primary rat myometrial and equine uterine epithelial cells. Functional analysis of changes in junctional communication induced by 8-bromo-cAMP was monitored by a fluorescence recovery after photobleaching assay in subconfluent cultures in the presence or absence of 1.0 mm 1-octanol (an agent which uncouples cells by closing gap junction channels). Communicating cells treated with 1.0 mm 8-bromo-cAMP alone exhibited significant increases in the percent of fluorescence recovery which were detected within 1–3 min depending on cell type, and junctional communication remained significantly elevated for up to 24 hr. Addition of 1.0 mm 8-bromo-cAMP to cultured cells, which were uncoupled with 1.0 mm octanol for 1 min, exhibited partial restoration of gap junctional permeability beginning within 3–5 min. Identical treatments were performed on cultures that were subsequently processed for indirect immunofluorescence to monitor Cx43 distribution. The changes in junctional permeability of cells correlated with changes in the distribution of immunoreactive Cx43. Cells treated for 2 hr with 10 m monensin exhibited a reduced communication rate which was accompanied by increased vesicular cytoplasmic Cx43 staining and reduced punctate surface staining of junctional plaques. Addition of 1.0 mm 8-bromo-cAMP to these cultures had no effect on the rate of communication or the distribution of Cx43 compared to cultures treated with monensin alone. These data suggest that an effect of cyclic AMP on Cx43 gap junctions is to promote increases in gap junctional permeability by increasing trafficking and/or assembly of Cx43 to plasma membrane gap junctional plaques.We acknowledge the technical assistance of Richard Lewis and Meghan Abella. We thank Dr. Hugh Dookwah for contributions to the myometrial cell isolation protocol and Drs. Stephen H. Safe, Timothy D. Phillips, and Evelyn Tiffany-Castiglioni for helpful discussions. This work was funded by NIH (HD-26182, P42-ES04917, ES05871-01A1), the March of Dimes Birth Defects Foundation Basic Research grant #1-0796, and USDA 92-37203-7952.     

The DNA sequence selectivity of maltolato-containing cisplatin analogues in purified plasmid DNA and in intact human cells

Cisplatin analogues with an attached DNA binding moiety have a higher affinity for DNA, but often suffer from poor aqueous solubility. In this study we examined the DNA sequence specificity of more soluble cisplatin analogues containing the maltolato leaving group in both purified DNA and in intact human cells. In both environments the DNA sequence specificity of these analogues was very similar to cisplatin. However, in purified DNA a higher concentration of the two maltolato-containing analogues was needed to achieve a similar level of DNA damage as cisplatin. This difference in reactivity was not observed in intact cells as the two maltolato-containing complexes were capable of producing a similar level of damage as cisplatin at comparable concentrations. This was consistent with the IC₅₀ values obtained for both cisplatin and the maltolato compounds which were also similar. This study indicated that maltolato can be utilised as the leaving group to increase the aqueous solubility of cisplatin analogues without reducing their biological activity.