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Biased biological functions of horizontally transferred genes in prokaryotic genomes

Nature Genetics volume 36, pages 760–766 (2004)Cite this article

A Corrigendum to this article was published on 01 October 2004

Abstract

Horizontal gene transfer is one of the main mechanisms contributing to microbial genome diversification1,2,3. To clarify the overall picture of interspecific gene flow among prokaryotes, we developed a new method for detecting horizontally transferred genes and their possible donors by Bayesian inference with training models for nucleotide composition. Our method gives the average posterior probability (horizontal transfer index) for each gene sequence, with a low horizontal transfer index indicating recent horizontal transfer. We found that 14% of open reading frames in 116 prokaryotic complete genomes were subjected to recent horizontal transfer. Based on this data set, we quantitatively determined that the biological functions of horizontally transferred genes, except mobile element genes, are biased to three categories: cell surface, DNA binding and pathogenicity-related functions. Thus, the transferability of genes seems to depend heavily on their functions.

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Figure 1: Donor identification of horizontally transferred genes in Neisseria meningitidis.
Figure 2: Proportion of horizontally transferred (HT) genes in each functional category.

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Acknowledgements

We thank N. Tsuboi for coding the horizontally transferred gene detection programs; N. Nishinomiya, M. Matsuo and R. Yamaguchi for technical assistance; and K. Ikeo, J.S. Hwang and R. Barrero for their comments and suggestions. T.I. and T.G. were supported in part by grants from the New Energy and Industrial Technology Development Organization and the Ministry of Economy, Technology, and Industry of Japan. T.I., T.G. and H.M. were supported by grants from the Ministry of Education, Sports, Culture, Science and Technology of Japan.

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Author notes

  1. Yoji Nakamura

    Present address: Graduate School of Information Science and Technology, Hokkaido University, 9 Nishi, 14 Kita, Kita-ku, Sapporo, Hokkaido, 060-0814, Japan

Authors and Affiliations

  1. Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan

    Yoji Nakamura & Takashi Gojobori

  2. Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, TIME24 Bldg. 10F, 2-45 Aomi, Koto-ku, Tokyo, 135-0064, Japan

    Takeshi Itoh & Takashi Gojobori

  3. Genome Research Department, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Takeshi Itoh

  4. Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan

    Hideo Matsuda

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  1. Yoji Nakamura
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  2. Takeshi Itoh
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Corresponding author

Correspondence to Takashi Gojobori.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Relationship between the total number of examined ORFs and the proportion of HT genes in a genome. (PDF 60 kb)

Supplementary Table 1

Sensitivities and selectivities of HT detection methods. (PDF 2 kb)

Supplementary Table 2

Possible pathogenicity islands detected in this study. (PDF 9 kb)

Supplementary Table 3

Subroles containing frequently transferred genes. (PDF 6 kb)

Supplementary Table 4

Species having an abundance of regulatory function HT genes. (PDF 2 kb)

Supplementary Note (PDF 4 kb)

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Nakamura, Y., Itoh, T., Matsuda, H. et al. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36, 760–766 (2004). https://doi.org/10.1038/ng1381

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