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Atomic Force Microscopy Dissects the Hierarchy of Genome Architectures in Eukaryote, Prokaryote, and Chloroplast

Published online by Cambridge University Press:  18 January 2007

R.L. Ohniwa ,
K. Morikawa ,
J. Kim ,
T. Kobori ,
K. Hizume ,
R. Matsumi ,
H. Atomi ,
T. Imanaka ,
T. Ohta  and
C. Wada
...Show all authors
R.L. Ohniwa
Affiliation:
Kyoto University Graduate School of Biostudies, Sakyo-ku, Kyoto 606-8502, Japan
K. Morikawa
Affiliation:
Institute for Basic Medical Sciences, Tsukuba University, Tsukuba, Japan
J. Kim
Affiliation:
Kyoto University Graduate School of Biostudies, Sakyo-ku, Kyoto 606-8502, Japan
T. Kobori
Affiliation:
Kyoto University Graduate School of Biostudies, Sakyo-ku, Kyoto 606-8502, Japan
K. Hizume
Affiliation:
Kyoto University Graduate School of Biostudies, Sakyo-ku, Kyoto 606-8502, Japan
R. Matsumi
Affiliation:
Kyoto University Graduate School of Engineering, Katsura, Kyoto, Japan
H. Atomi
Affiliation:
Kyoto University Graduate School of Engineering, Katsura, Kyoto, Japan
T. Imanaka
Affiliation:
Kyoto University Graduate School of Engineering, Katsura, Kyoto, Japan
T. Ohta
Affiliation:
Institute for Basic Medical Sciences, Tsukuba University, Tsukuba, Japan
C. Wada
Affiliation:
Kyoto University Graduate School of Biostudies, Sakyo-ku, Kyoto 606-8502, Japan
S.H. Yoshimura
Affiliation:
Kyoto University Graduate School of Biostudies, Sakyo-ku, Kyoto 606-8502, Japan
K. Takeyasu
Affiliation:
Kyoto University Graduate School of Biostudies, Sakyo-ku, Kyoto 606-8502, Japan
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Abstract

Because of its applicability to biological specimens (nonconductors), a single-molecule-imaging technique, atomic force microscopy (AFM), has been particularly powerful for visualizing and analyzing complex biological processes. Comparative analyses based on AFM observation revealed that the bacterial nucleoids and human chromatin were constituted by a detergent/salt-resistant 30–40-nm fiber that turned into thicker fibers with beads of 70–80 nm diameter. AFM observations of the 14-kbp plasmid and 110-kbp F plasmid purified from Escherichia coli demonstrated that the 70–80-nm fiber did not contain a eukaryotic nucleosome-like “beads-on-a-string” structure. Chloroplast nucleoid (that lacks bacterial-type nucleoid proteins and eukaryotic histones) also exhibited the 70–80-nm structural units. Interestingly, naked DNA appeared when the nucleoids from E. coli and chloroplast were treated with RNase, whereas only 30-nm chromatin fiber was released from the human nucleus with the same treatment. These observations suggest that the 30–40-nm nucleoid fiber is formed with a help of nucleoid proteins and RNA in E. coli and chroloplast, and that the eukaryotic 30-nm chromatin fiber is formed without RNA. On the other hand, the 70–80-nm beaded structures in both E. coli and human are dependent on RNA.

Keywords

atomic force microscopynucleoidgenome architectureEscherichia coliStaphylococcus aureusClostridium perfringensChloroplastHeLa cell
Type
Research Article
Information
Microscopy and Microanalysis , Volume 13 , Issue 1: Special Issue: Environmental, Industrial, and AppliedMicrobiology , February 2007 , pp. 3 - 12
Copyright
2007 Microscopy Society of America

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