Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes.
Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes.
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DOI：
10.1186/1471-2105-7-257
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发表时间：
2006-05-18
影响因子：
3
通讯作者：
Garcia-Vallve S
中科院分区：
文献类型：
--
作者：
Pasamontes A;Garcia-Vallve S
蛋白质中的氨基酸并不是平等使用的。蛋白质氨基酸组成的一些差异存在于物种之间（主要是由于核苷酸组成和生活方式），一些差异存在于同一物种的蛋白质之间（例如与蛋白质功能，表达或亚细胞定位有关）。由于有几个因素导致蛋白质中氨基酸的不同使用，因此很难分析这些差异并区分每个因素的贡献。使用多路方法Tucker3，我们分析了一组64个邻位基团的蛋白质存在于62个古细菌和细菌的氨基组成。该数据集对应于必需蛋白质，如核糖体蛋白、tRNA合成酶和翻译起始或延伸因子，这些蛋白质在所有分析的物种中都是常见的。Tucker3模型可用于研究物种内和物种间的氨基酸变异性，并考虑到数据集的三维性。我们发现，蛋白质氨基酸组成背后的主要因素与所分析的生物体或蛋白质功能无关。这个因素必须与每种氨基酸的生化特性有关。非核糖体蛋白和核糖体蛋白（富含精氨酸和赖氨酸）之间的差异是物种内氨基酸组成差异的主要因素，而G+C含量和最佳生长温度是物种间氨基酸利用差异的主要因素。我们表明，多途径的方法是有用的比较几组orthopathic蛋白质的氨基酸组成，从同一组物种。这种数据集对于检测物种之间和物种内部的差异非常有用。
Amino acids in proteins are not used equally. Some of the differences in the amino acid composition of proteins are between species (mainly due to nucleotide composition and lifestyle) and some are between proteins from the same species (related to protein function, expression or subcellular localization, for example). As several factors contribute to the different amino acid usage in proteins, it is difficult both to analyze these differences and to separate the contributions made by each factor. Using a multi-way method called Tucker3, we have analyzed the amino composition of a set of 64 orthologous groups of proteins present in 62 archaea and bacteria. This dataset corresponds to essential proteins such as ribosomal proteins, tRNA synthetases and translational initiation or elongation factors, which are common to all the species analyzed. The Tucker3 model can be used to study the amino acid variability within and between species by taking into consideration the tridimensionality of the data set. We found that the main factor behind the amino acid composition of proteins is independent of the organism or protein function analyzed. This factor must be related to the biochemical characteristics of each amino acid. The difference between the non-ribosomal proteins and the ribosomal proteins (which are rich in arginine and lysine) is the main factor behind the differences in amino acid composition within species, while G+C content and optimal growth temperature are the main factors behind the differences in amino acid usage between species. We show that a multi-way method is useful for comparing the amino acid composition of several groups of orthologous proteins from the same group of species. This kind of dataset is extremely useful for detecting differences between and within species.
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DOI：
10.1098/rspb.2000.1397
发表时间：
2001-03-07
影响因子：
4.7
作者：
Hurst, LD;Merchant, AR
通讯作者：
Merchant, AR
影响因子：
14.9
作者：
Lynn, DJ;Singer, GAC;Hickey, DA
通讯作者：
Hickey, DA
影响因子：
14.9
作者：
Kreil, DP;Ouzounis, CA
通讯作者：
Ouzounis, CA
影响因子：
14.9
作者：
Makarova, KS;Aravind, L;Koonin, EV
通讯作者：
Koonin, EV
影响因子：
5.7
作者：
Jelinska, C;Conroy, MJ;White, MF
通讯作者：
White, MF