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With the availability of complete genome sequences, microbial research has entered a new era, to understand various cellular functions as a network of proteins encoded on the genome. We study the basic cellular functions of model bacteria, Bacillus subtilis and Echerichia coli, as a system. Therefore, we are implementing novel research methods such as whole genome expression analysis using DNA chips, analysis of trace amounts of protein by mass spectrometry, and analysis of protein localization in cells by fluorescence microscopy (Fig. 1).
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- Studies on the genetic system essential for the B. subtilis growth
- Functional analysis of essential genes with unknown function: About 4100 genes are encoded in the B. subtilis genome. In order to identify functionally unknown genes which account for about half of the genes in this organism, we have generated mutants for all unanalyzed genes. As a result, about 20 functionally uncharacterized genes were found to be essential for growth (Kobayashi et al. 2003). Recently, one of these genes was shown to serve as an important factor for fatty acid synthesis.
- Analysis of GTP-binding protein: We found that 6 different bacterial GTP binding proteins are essential for B. subtilis growth (Morimoto et al. 2002). We recently showed that one of these proteins is involved in the assembly of 50S ribosome subunit, indicating that our understanding of basic cellular process such as translation is still incomplete (Matsuo et al. 2006) (Fig. 2).
- Studies on the genetic systems regulating bacterial cell cycle: We also study the genetic systems involved in genome replication and partition and cell division, which are key functions in bacterial cell cycle (Noirot-Gros et al. 2006; Kawai et al. 2006). Recently we have been attempting to elucidate the molecular mechanisms using the protein complex analysis method we have developed (Ishikawa et al. 2006) (Fig. 3).
- Studies on the regulatory network of gene expression in B. subtilis and E. coli
Expression of genes is regulated in a coordinated manner by the action of about 250 DNA binding transcriptional regulators in B. subtilis and E. coli cells. We are attempting to clarify the whole network by using a combination of DNA array analysis and genetic methods. In particular we studied function of two-component regulatory systems, which recognizes environmental signals and controls the expression of genes required for environmental adaptation (Ohki et al. 2003; Tanaka et al. 2003). Furthermore, we have recently started a new approach to explore the in vivo distribution of DNA binding proteins on the genome by using chromatin immunoprecipitation coupled with high density tiling chip (ChIP-chip analysis; Oshima et al. 2006).
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- Ishikawa et al., A new FtsZ-interacting protein, YlmF, complements the activity of FtsA during progression of cell division in Bacillus subtilis. Mol Microbiol 60, 1364-1380, 2006
- Kawai et al., Bacillus subtilis EzrA and FtsL synergistically regulate FtsZ ring dynamics during cell division. Microbiology 152, 1129-1141, 2006
- Kobayashi et al., Essential Bacillus subtilis genes, Proc Natl Acad Sci USA 100, 4678-4683, 2003
- Matsuo et al., The GTP-binding protein YlqF participates in the late step of 50 S ribosomal subunit assembly in Bacillus subtilis. J Biol Chem 281, 8110-8117, 2006
- Morimoto et al., Six GTP-binding proteins of the Era/Obg family are essential for cell growth in Bacillus subtilis, Microbiology 148, 3539-3552, 2002
- Noirot-Gros et al., Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus subtilis. Proc Natl Acad Sci USA 103, 2368-2373, 2006
- Ohki et al., The BceRS two-component regulatory system induces expression of the bacitracin transporter, BceAB, in Bacillus subtilis. Mol Microbiol 49, 1135-1144, 2003
- Oshima et al., Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res, in press
- Tanaka et al., The Bacillus subtilis YufLM two-component system regulates the expression of the malate transporters MaeN (YufR) and YflS, and is essential for utilization of malate in minimal medium. Microbiology 149, 2317-2329, 2003
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Fig. 1 Outline of our research
Fig. 2 Research on GTP-bound proteins
Fig. 3 Research on protein complexes
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