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Molecular & Cellular Proteomics 3:780-787, 2004.
© 2004 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Only a Small Subset of the Horizontally Transferred Chromosomal Genes in Escherichia coli Are Translated into Proteins^*,S

Masato Taoka, Yoshio Yamauchi, Takashi Shinkawa, Hiroyuki Kaji, Wakana Motohashi, Hiroshi Nakayama^¶, Nobuhiro Takahashi^|| and Toshiaki Isobe^,,**,

From the Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan; Integrated Proteomics System Project, Pioneer Research on Genome the Frontier, MEXT, c/o Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan; ^¶ RIKEN (The Institute of Physical and Chemical Research), Hirosawa 2-1, Wako-shi, Saitama 351-0198, Japan; ^|| Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan; and ^** Division of Proteomics Research, The Institute of Medical Science, The University of Tokyo, Shiroganedai 4-6-1, Minato-ku, Tokyo 108-8639, Japan

Horizontally transferred genes are believed to play a critical role in the divergence of bacterial strains from a common ancestor, but whether all of these genes express functional proteins in the cell remains unknown. Here, we used an integrated LC-based protein identification technology to analyze the proteome of Escherichia coli strain K12 (JM109) and identified 1,480 expressed proteins, which are equivalent to 35% of the total open reading frames predicted in the genome. This subset contained proteins with cellular abundance of several dozens to hundreds of thousands of copies, and included nearly all types of proteins in terms of chemical characteristics, subcellular distribution, and function. Interestingly, the subset also contained 138 of 164 gene products that are currently known to be essential for bacterial viability (84% coverage). However, the subset contained only a very small population (10%) of protein products from genes mapped within K-loops, which are "hot spots" for the integration of foreign DNAs within the K12 genome. On the other hand, these genes in K-loops appeared to be transcribed to RNAs almost as efficiently as the native genes in the bacterial cell as monitored by DNA microarray analysis, raising the possibility that most of the recently acquired foreign genes are inadequate for the translational machinery for the native genes and do not generate functional proteins within the cell.

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