Abstract
A series of structome analyses, that is, quantitative and three-dimensional structural analysis of a whole cell at the electron microscopic level, have already been achieved individually in Exophiala dermatitidis, Saccharomyces cerevisiae, Mycobacterium tuberculosis, Myojin spiral bacteria, and Escherichia coli. In these analyses, sample cells were processed through cryo-fixation and rapid freeze-substitution, resulting in the exquisite preservation of ultrastructures on the serial ultrathin sections examined by transmission electron microscopy. In this paper, structome analysis of non pathogenic Mycolicibacterium smegmatis, basonym Mycobacterium smegmatis, was performed. As M. smegmatis has often been used in molecular biological experiments and experimental tuberculosis as a substitute of highly pathogenic M. tuberculosis, it has been a task to compare two species in the same genus, Mycobacterium, by structome analysis. Seven M. smegmatis cells cut into serial ultrathin sections, and, totally, 220 serial ultrathin sections were examined by transmission electron microscopy. Cell profiles were measured, including cell length, diameter of cell and cytoplasm, surface area of outer membrane and plasma membrane, volume of whole cell, periplasm, and cytoplasm, and total ribosome number and density per 0.1 fl cytoplasm. These data are based on direct measurement and enumeration of exquisitely preserved single cell structures in the transmission electron microscopy images, and are not based on the calculation or assumptions from biochemical or molecular biological indirect data. All measurements in M. smegmatis, except cell length, are significantly higher than those of M. tuberculosis. In addition, these data may explain the more rapid growth of M. smegmatis than M. tuberculosis and contribute to the understanding of their structural properties, which are substantially different from M. tuberculosis, relating to the expression of antigenicity, acid-fastness, and the mechanism of drug resistance in relation to the ratio of the targets to the corresponding drugs. In addition, data obtained from cryo-transmission electron microscopy examination were used to support the validity of structome analysis. Finally, our data strongly support the most recent establishment of the novel genus Mycolicibacterium, into which basonym Mycobacterium smegmatis has been classified.
Highlights
Mycolicibacterium smegmatis is a rapid-growing bacterium and previously belonged to the genus Mycobacterium as basonym Mycobacterium smegmatis, to which many pathogenic mycobacteria, including M. tuberculosis, a causative agent of tuberculosis, and M. leprae, a causative agent of leprosy, are belonging (Gupta et al, 2018; Oren and Garrity, 2018)
Cell length measured in CryoTEM examination for 61 M. smegmatis cells ranged from 1.08 to 6.27 μm, with average 3.46 ± 1.40 μm, which was similar to serial ultrathin section examination (Table S1)
It is revealed that M. smegmatis had belonged to the genus Mycobacterium, M. smegmatis is less similar to M. tuberculosis in the aspect of cell biology with significant differences, including acid-fastness, cell diameter, cell length, surface areas, cell volume, total ribosome number, and ribosome density
Summary
Mycolicibacterium smegmatis is a rapid-growing bacterium and previously belonged to the genus Mycobacterium as basonym Mycobacterium smegmatis, to which many pathogenic mycobacteria, including M. tuberculosis, a causative agent of tuberculosis, and M. leprae, a causative agent of leprosy, are belonging (Gupta et al, 2018; Oren and Garrity, 2018). We have already reported structome analysis data on Exophiala dermatitidis (Yamaguchi, 2006), Saccharomyces cerevisiae (Yamaguchi et al, 2011), M. tuberculosis (Yamada et al, 2015), Myojin spiral bacteria (Yamaguchi et al, 2016b), Escherichia coli (Yamada et al, 2017), and Myojin amorphous bacteria (Yamaguchi et al, 2018) In these previous studies, samples were prepared through rapid-freezing and freezesubstitution, and fundamental quantitative data of the single cells were provided with examination of serial ultrathin sections by transmission electron microscope (TEM), including cell diameter, length, volume of whole cell and cytoplasm, surface area, and cytoplasmic ribosome number. M. tuberculosis, Myojin spiral bacteria, and Myojin amorphous bacteria have much lower cytoplasmic ribosome density with lower total ribosome number in a much smaller cytoplasmic volume
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