論文 - 鈴木　治夫

Comparison of correspondence analysis methods for synonymous codon usage in bacteria.

Suzuki H, Brown CJ, Forney LJ, Top EM

DNA research : an international journal for rapid publication of reports on genes and genomes （DNA Research）  15 （ 6 ） 357 - 65 2008年12月

研究論文（学術雑誌）, 査読有り,  ISSN  1340-2838

　概要を見る

Synonymous codon usage varies both between organisms and among genes within a genome, and arises due to differences in G + C content, replication strand skew, or gene expression levels. Correspondence analysis (CA) is widely used to identify major sources of variation in synonymous codon usage among genes and provides a way to identify horizontally transferred or highly expressed genes. Four methods of CA have been developed based on three kinds of input data: absolute codon frequency, relative codon frequency, and relative synonymous codon usage (RSCU) as well as within-group CA (WCA). Although different CA methods have been used in the past, no comprehensive comparative study has been performed to evaluate their effectiveness. Here, the four CA methods were evaluated by applying them to 241 bacterial genome sequences. The results indicate that WCA is more effective than the other three methods in generating axes that reflect variations in synonymous codon usage. Furthermore, WCA reveals sources that were previously unnoticed in some genomes; e.g. synonymous codon usage related to replication strand skew was detected in Rickettsia prowazekii. Though CA based on RSCU is widely used, our evaluation indicates that this method does not perform as well as WCA.

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Modelling the spatial dynamics of plasmid transfer and persistence.

Krone SM, Lu R, Fox R, Suzuki H, Top EM

Microbiology (Reading, England) （Microbiology）  153 （ Pt 8 ） 2803 - 16 2007年08月

研究論文（学術雑誌）, 査読有り,  ISSN  1350-0872

　概要を見る

Bacterial plasmids are extra-chromosomal genetic elements that code for a wide variety of phenotypes in their bacterial hosts and are maintained in bacterial communities through both vertical and horizontal transfer. Current mathematical models of plasmid-bacteria dynamics, based almost exclusively on mass-action differential equations that describe these interactions in completely mixed environments, fail to adequately explain phenomena such as the long-term persistence of plasmids in natural and clinical bacterial communities. This failure is, at least in part, due to the absence of any spatial structure in these models, whereas most bacterial populations are spatially structured in microcolonies and biofilms. To help bridge the gap between theoretical predictions and observed patterns of plasmid spread and persistence, an individual-based lattice model (interacting particle system) that provides a predictive framework for understanding the dynamics of plasmid-bacteria interactions in spatially structured populations is presented here. To assess the accuracy and flexibility of the model, a series of experiments that monitored plasmid loss and horizontal transfer of the IncP-1β plasmid pB10:: rfp in Escherichia coli K12 and other bacterial populations grown on agar surfaces were performed. The model-based visual patterns of plasmid loss and spread, as well as quantitative predictions of the effects of different initial parental strain densities and incubation time on densities of transconjugants formed on a 2D grid, were in agreement with this and previously published empirical data. These results include features of spatially structured populations that are not predicted by mass-action differential equation models. © 2007 SGM.

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Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus.

Fujishima K, Komasa M, Kitamura S, Suzuki H, Tomita M, Kanai A

DNA research : an international journal for rapid publication of reports on genes and genomes （DNA Research）  14 （ 3 ） 91 - 102 2007年06月

研究論文（学術雑誌）, 査読有り,  ISSN  1340-2838

　概要を見る

Proteins play a critical role in complex biological systems, yet about half of the proteins in publicly available databases are annotated as functionally unknown. Proteome-wide functional classification using bioinformatics approaches thus is becoming an important method for revealing unknown protein functions. Using the hyperthermophilic archaeon Pyrococcus furiosus as a model species, we used the support vector machine (SVM) method to discriminate DNA/RNA-binding proteins from proteins with other functions, using amino acid composition and periodicities as feature vectors. We defined this value as the composition score (CO) and periodicity score (PD). The P. furiosus proteins were classified into three classes (I-III) on the basis of the two-dimensional correlation analysis of CO score and PD score. As a result, approximately 87 of the functionally known proteins categorized as class I proteins (CO score + PD score > 0.6) were found to be DNA/RNA-binding proteins. Applying the two-dimensional correlation analysis to the 994 hypothetical proteins in P. furiosus, a total of 151 proteins were predicted to be novel DNA/RNA-binding protein candidates. DNA/RNA-binding activities of randomly chosen hypothetical proteins were experimentally verified. Six out of seven candidate proteins in class I possessed DNA/RNA-binding activities, supporting the efficacy of our method. © The Author 2007. Kazusa DNA Research Institute.

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Region-specific insertion of transposons in combination with selection for high plasmid transferability and stability accounts for the structural similarity of IncP-1 plasmids.

Sota M, Tsuda M, Yano H, Suzuki H, Forney LJ, Top EM

Journal of bacteriology （Journal of Bacteriology）  189 （ 8 ） 3091 - 8 2007年04月

研究論文（学術雑誌）, 査読有り,  ISSN  0021-9193

　概要を見る

The overall architecture of IncP-1 plasmids is very conserved in that the accessory genes are typically located in one or two specific regions: between oriV and trfA and between the tra and trb operons. Various hypotheses have been formulated to explain this, but none have been tested experimentally. We investigated whether this structural similarity is due to region-specific transposition alone or also is reliant on selection for plasmids with insertions limited to these two regions. We first examined the transposition of Tn21Km into IncP-1β plasmid pBP136 and found that most Tn21Km insertions (67%) were located around oriV. A similar experiment using the oriV region of IncP-1β plasmid pUO1 confirmed these results. We then tested the transferability, stability, and fitness cost of different pBP136 derivatives to determine if impairment of these key plasmid characters explained the conserved plasmid architecture. Most of the pBP136 derivatives with insertions in transfer genes were no longer transferable. The plasmids with insertions in the oriV-trfA and tra-trb regions were more stable than other plasmid variants, and one of these also showed a significantly lower fitness cost. In addition, our detailed sequence analysis of IncP-1 plasmids showed that Tn402/5053-like transposons are situated predominantly between the tra and trb operons and close to the putative resolution site for the ParA resolvase, a potential hot spot for those transposons. Our study presents the first empirical evidence that region-specific insertion of transposons in combination with selection for transferable and stable plasmids explains the structural similarity of IncP-1 plasmids. Copyright © 2007, American Society for Microbiology. All Rights Reserved.

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Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria.

Suzuki H, Saito R, Tomita M

EURASIP journal on bioinformatics & systems biology （Eurasip Journal on Bioinformatics and Systems Biology）  2007   61374 2007年

研究論文（学術雑誌）, 査読有り,  ISSN  1687-4145

　概要を見る

G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlation among different genomes. Here, we applied Shannon entropy from information theory to measure the degree of GC3 bias and that of synonymous codon usage bias of each gene. The strength of the correlation of GC3 with synonymous codon usage bias, quantified by a correlation coefficient, varied widely among bacterial genomes, ranging from -0.07 to 0.95. Previous analyses suggesting that the relationship between GC3 and synonymous codon usage bias is independent of species are thus inconsistent with the more detailed analyses obtained here for individual species.

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A problem in multivariate analysis of codon usage data and a possible solution.

Suzuki H, Saito R, Tomita M

FEBS letters （FEBS Letters）  579 （ 28 ） 6499 - 504 2005年11月

研究論文（学術雑誌）, 査読有り,  ISSN  0014-5793

　概要を見る

Multivariate analyses are often used to identify major trends of variation in synonymous codon usage among genes. These analyses need to be performed on properly normalized codon usage data to avoid biases masking this synonymous variation, i.e., gene length, amino acid usage, and codon degeneracy; however, previous studies have failed to do so. In this paper, we demonstrate that the use of alternative normalized data (called 'relative adaptiveness' in the literature) can avoid all these biases and furthermore, can identify more trends of variation among genes, including GC-ending codon usage, GT-ending codon usage, and gene expression level. © 2005 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.

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A comprehensive software suite for the analysis of cDNAs.

Arakawa K, Suzuki H, Fujishima K, Fujimoto K, Ueda S, Matsui M, Tomita M

Genomics, proteomics & bioinformatics （Genomics, Proteomics and Bioinformatics）  3 （ 3 ） 179 - 88 2005年08月

研究論文（学術雑誌）, 査読有り,  ISSN  1672-0229

　概要を見る

We have developed a comprehensive software suite for bioinformatics research of cDNAs; it is aimed at rapid characterization of the features of genes and the proteins they code. Methods implemented include the detection of translation initiation and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative modeling of the structures of product proteins, prediction of alternative splice forms, and metabolic pathway reconstruction.

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The 'weighted sum of relative entropy': a new index for synonymous codon usage bias.

Suzuki H, Saito R, Tomita M

Gene （Gene）  335 （ 1-2 ） 19 - 23 2004年06月

研究論文（学術雑誌）, 査読有り,  ISSN  0378-1119

　概要を見る

Shannon entropy from information theory has been applied to estimate the degree of deviation from equal usage of synonymous codons; however, previous attempts have failed to take into account all three aspects of amino acid usage, i.e. (i) the number of distinct amino acids, (ii) their relative frequencies, and (iii) their degree of codon degeneracy. A new index taking into account all of these aspects is proposed. The index, designated as the 'weighted sum of relative entropy' (Ew), is defined as the sum of the relative entropy of each amino acid weighted by its relative frequency in the sequence. In this paper, we demonstrate that Ew allows us to avoid some amino acid usage biases and can yield results contradictory to those obtained by previous methods. © 2004 Elsevier B.V. All rights reserved.

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