Seiji KOJIMA, Assistant Professor, Tohoku University

Seiji KOJIMA, Ph.D.

Assistant Professor


Cell Biology of the Microbial Cell Surfaces

¡General Interest and Research Summary

Interior and exterior of living organism is separated by cell envelope. Therefore, the structure and function of the cell envelope are critical for various aspects of cellular activity such as transport, morphogenesis, response to extracellular environment, and so on. I've been interested in the cell surface of Gram-negative bacteria, which comprises cytoplasmic membrane, peptidoglycan (cell wall) layer, and outer membrane. During my Ph. D. study, I examined molecular basis of the interaction between the outer membrane and underlying peptidoglycan layer, an ganchorh crucial for maintaining structural integrity of the outer membrane (Kojima et al. 2010, 2011). As a postdoc, with the aim of understanding quantitatively the function of the outer membrane, I examined the permeability of the outer membrane by analyzing the movement of substances across the outer membrane, using ƒÀ-lactam antibiotics as substrates (Kojima & Nikaido 2013, 2014).

Because the outer membrane directly affects the speed of flux of various substances to/from the cell, its permeability is quantitatively linked to the cellular physiology, survival and responses to the external environment. My current researches focus on the molecular basis of the permeability and stability of the outer membrane, in the context of nutrient uptake and also the antibiotic resistance of Gram-negative bacteria. Also, I started recently the research on the outer membrane of chloroplasts, an organelle descended from an endosymbiotic cyanobacterium (Gram-negative bacteria that conduct oxygenic photosynthesis). The aim of this research is to understand how the function of the outer membrane has changed (or preserved) during the course of evolution from free living cyanobacteria to chloroplasts.

¡Current Projects

1) Mechanism of antibiotic resistance of Gram-negative bacteria
Drugs must first penetrate the outer membrane before reaching its targets. Outer membrane of Gram-negative bacteria serves as the permeability barrier that inhibits the drug entry, thereby highly contributes to antibiotic resistance. I study on the molecular mechanisms that determine the outer membrane permeability.
yReferenceFKojima et al. 2013, 2014, Sugawara et al. 2016, Kowata et al. 2016z

2) Function of the outer membrane of primitive chloroplast.
During the course of evolution from an endosymbiotic cyanobacterium to the chloroplast, the function of the outer membrane changed from permeability barrier to an interface that connects two metabolic entities, the chloroplast and host cell. I want to know how this functional alteration was possible. I study on the outer membrane of primitive chloroplast (chloroplast of Cyanophora paradoxa) that retains the peptidoglycan layer between its inner and outer membrane.
yReferenceFKowata et al. 2017, Kojima et al. 2016, 2018z

3) Outer membrane structure and function of ruminal bacteria.
Ecology and metabolic activity of ruminal bacteria are directly linked to the physiology of ruminant, such as cow or sheep. I study on the structure and function of the outer membrane of a strictly anaerobic Gram-negative bacterium Selenomonas ruminantium which is one of the dominant bacterial species in rumen. Currently I focus on the mechanism of nutrient uptake across the outer membrane of this bacterium.
yReferenceFKojima et al. 2010, 2011, 2016z

¡Selected Publication


Kojima S, Iwamoto M, Oiki S, Tochigi S, Takahashi H
Thylakoid membranes contain a non-selective channel permeable to small organic molecules.
J. Biol. Chem. (doi: 10.1074/jbc.RA118.002367)


Kowata H, Tochigi S, Takahashi H, Kojima S
Outer membrane permeability of cyanobacterium Synechocystis sp. PCC 6803: studies of passive diffusion of small organic nutrients reveal the absence of classical porins and intrinsically low permeability.
J. Bacteriol. 199:e00371-17


Kojima S, Muramoto K, Kusano T
Outer membrane proteins derived from non-cyanobacterial lineage cover the peptidoglycan of Cyanophora paradoxa cyanelles and serve as a cyanelle diffusion channel.
J. Biol. Chem. 291:20198-20209.

Sugawara E, Kojima S, Nikaido H
Klebsiella pneumoniae major porins OmpK35 and OmpK36 allow more efficient diffusion of ƒÀ-lactams than their Escherichia coli homologs OmpF and OmpC.
J. Bacteriol. DOI:10.1128/JB.00590-16

Kojima S, Hayashi K, Tochigi S, Kusano T, Kaneko J, Kamio Y
Peptidoglycan-associated outer membrane protein Mep45 of rumen anaerobe Selenomonas ruminantium forms a non-specific diffusion pore via its C-terminal transmembrane domain.
Biosci. Biotech. Biochem. 80:1954-1959.

Kowata H, Tochigi S, Kusano T, Kojima S
Quantitative measurement of the outer membrane permeability in Escherichia coli lpp and tol-pal mutants defines the significance of Tol-Pal function for maintaining drug resistance.
J. Antibiotics. DOI:10.1038/ja.2016.50.


Kaneko J, S. Yamada-Narita, N. Abe, T. Onodera, E. Kan, S. Kojima, T. Miyazaki, Y. Yamamoto, A. Oguchi, A. Ankai, N. Ichikawa, H. Nakazawa, S. Fukui, M. Takahashi, S. Yamazaki, N. Fujita & Y. Kamio
Complete genome sequence of Selenomonas ruminantium subsp. lactilytica will accelerate further understanding of the nature of the class Negativicutes.
FEMS Microbiol Lett 362(9)1-6.


Kojima S, Nikaido H
High salt concentrations increase permeability through OmpC channels of Escherichia coli.
J. Biol. Chem. 289:26464-26473


Kojima S, Nikaido H
Permeation rates of penicillins indicate that Escherichia coli porins function principally as nonspecific channels.
Proc Natl Acad Sci U S A 110(28): E2629-E2634


Kojima S, Kaneko J, Abe N, Takatsuka Y, Kamio Y
Cadaverine covalently linked to the peptidoglycan serves as the correct constituent for the anchoring mechanism between the outer membrane and peptidoglycan in Selenomonas ruminantium.
J Bacteriol 193(9): 2347-2350


Kojima S, Ko K.C., Takatsuka Y, Abe N, Kaneko J, Itoh Y, Kamio Y
Cadaverine covalently linked to peptidoglycan is required for interaction between the peptidoglycan and the periplasm-exposed S-layer-homologous domain of major outer membrane protein Mep45 in Selenomonas ruminantium.
J Bacteriol 192(22): 5953-5961