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Single-Cell and Single-Molecule Analysis of Microorganism

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 10052

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Special Issue Editor

Prof. Dr. Kunio Takeyasu

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Guest Editor

Graduate School of Biostudies, Kyoto University, Yoshida-Konoe Sakyo-Ku, Kyoto 606-8531, Japan
Interests: single molecule imaging of DNA, RNA, and protein; genome architecture of bacteria, archaea, and eukarya; biological application of atomic force microscopy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Historically, molecular studies of replication, transcription and translation mechanisms of viruses and bacteria have established the foundation (principles and theories) of eukaryotic molecular biology. Recent developments of cell/molecular analytical technologies have paved the way for the identification of a variety of individual molecular and cellular events. Among them, single cell/molecular imaging and manipulation techniques have been contributing to a physicochemical as well as structural basis for our understanding of such events.

This Special Issue will focus upon Nanobiology of Viruses, Microbe, and Intracellular Organelles, with special attention to the structural basis of their activities such as cell cycle, dynamic intracellular structures with cytoskeletons, genome folding, and others. Investigations using single cell/molecular imaging and manipulation techniques combined with other analytical methods will showcase their power to elucidate key principles of folding and interaction of biological macromolecules. Furthermore, comparisons of the data obtained from these innovative approaches with data related to eukaryotic systems will provide insights into molecular and cell biology in general.

Prof. Dr. Kunio Takeyasu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

Single-molecule imaging
Single-molecule manipulation
Ultra resolution microscopy
RNA virus genome
DNA virus genome
Bacteria
Archaea
Protozoa
Mitochondria
Chloroplast
Genome structure
Cytoskeleton
Membrane structure

Published Papers (4 papers)

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Research

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18 pages, 6654 KiB

Open AccessArticle

A Case Study of the Morphological and Molecular Variation within a Ciliate Genus: Taxonomic Descriptions of Three Dysteria Species (Ciliophora, Cyrtophoria), with the Establishment of a New Species

by Xuetong Zhao, Hui Zhang, Qianqian Zhang, Zhishuai Qu, Alan Warren, Di Wu and Xiangrui Chen

Int. J. Mol. Sci. 2022, 23(3), 1764; https://doi.org/10.3390/ijms23031764 - 3 Feb 2022

Cited by 3 | Viewed by 1547

Abstract

Three Dysteria species, D. crassipes Claparède & Lachmann, 1859; D. brasiliensis Faria et al., 1922; and D. paracrassipes n. sp., were collected from subtropical coastal waters of the East China Sea, near Ningbo, China. The three species were studied based on their living morphology, infraciliature, and molecular data. The new species D. paracrassipes n. sp. is very similar to D. crassipes in most morphological features except the preoral kinety, which is double-rowed in the new species (vs. single-rowed in D. crassipes). The difference in the small ribosomal subunit sequences (SSU rDNA) between these two species is 56 bases, supporting the establishment of the new species. The Ningbo population of D. crassipes is highly similar in morphology to other known populations. Nevertheless, the SSU rDNA sequences of these populations are very different, indicating high genetic diversity and potentially cryptic species. Dysteria brasiliensis is cosmopolitan with many described populations worldwide and four deposited SSU rDNA sequences. The present work supplies morphological and molecular information from five subtropical populations of D. brasiliensis that bear identical molecular sequences but show significant morphological differences. The findings of this study provide an opportunity to improve understanding of the morphological and genetic diversity of ciliates. Full article

(This article belongs to the Special Issue Single-Cell and Single-Molecule Analysis of Microorganism)

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14 pages, 12598 KiB

Open AccessArticle

“Take It or Leave It”—Factors Regulating Competence Development and DNA Uptake in Campylobacter jejuni

by Julia C. Golz and Kerstin Stingl

Int. J. Mol. Sci. 2021, 22(18), 10169; https://doi.org/10.3390/ijms221810169 - 21 Sep 2021

Cited by 3 | Viewed by 2146

Abstract

Campylobacter jejuni has a large adaptive potential due to enormous genetic exchange. Factors regulating natural transformation in this food-borne pathogen are largely unknown but of interest for the application of sustained reduction strategies in the food-processing industry. Using a single cell DNA uptake assay, we visualized that recognition of methylated C. jejuni DNA was essential for the first step of DNA uptake into a DNase resistant state. Transformation rates using a resistance marker correlated with the fraction of competent bacteria, harboring one to maximally four locations of active DNA uptake, not necessarily being located at the cell pole. Competence developed with rising pH between 6.5 and 7.5 under microaerobic conditions and was nearly insensitive towards growth temperatures between 32 °C and 42 °C, CO₂ concentrations ranging from 0 to 50% and growth rates. However, competence development was abolished at pH 5 or under aerobic stress conditions, in which the bacteria ceased growth but fully survived. The DNA uptake machinery in competent bacteria shut down at slightly acidic pH and was reversibly switched on upon neutralization. It was dependent on the proton motive force and, in contrast to competence development, slightly enhanced under aerobic conditions. The results suggest that natural transformation in C. jejuni occurs in the neutral and microaerobic intestinal environment for enhanced genetic diversity and pre-adaption before host switch. In addition, highly competent bacteria might be shed into the environment, still able to acquire genetic material for increased survival. Full article

(This article belongs to the Special Issue Single-Cell and Single-Molecule Analysis of Microorganism)

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13 pages, 2869 KiB

Open AccessArticle

Effects of Structural Isomers of Spermine on the Higher-Order Structure of DNA and Gene Expression

by Tomoki Kitagawa, Takashi Nishio, Yuko Yoshikawa, Naoki Umezawa, Tsunehiko Higuchi, Chwen-Yang Shew, Takahiro Kenmotsu and Kenichi Yoshikawa

Int. J. Mol. Sci. 2021, 22(5), 2355; https://doi.org/10.3390/ijms22052355 - 26 Feb 2021

Cited by 9 | Viewed by 2706

Abstract

Polyamines are involved in various biological functions, including cell proliferation, differentiation, gene regulation, etc. Recently, it was found that polyamines exhibit biphasic effects on gene expression: promotion and inhibition at low and high concentrations, respectively. Here, we compared the effects of three naturally occurring tetravalent polyamines, spermine (SPM), thermospermine (TSPM), and N⁴-aminopropylspermidine (BSPD). Based on the single DNA observation with fluorescence microscopy together with measurements by atomic force microscopy revealed that these polyamines induce shrinkage and then compaction of DNA molecules, at low and high concentrations, respectively. We also performed the observation to evaluate the effects of these polyamine isomers on the activity of gene expression by adapting a cell-free luciferase assay. Interestingly, the potency of their effects on the DNA conformation and also on the inhibition of gene expression activity indicates the highest for TSPM among spermine isomers. A numerical evaluation of the strength of the interaction of these polyamines with negatively charged double-strand DNA revealed that this ordering of the potency corresponds to the order of the strength of the attractive interaction between phosphate groups of DNA and positively charged amino groups of the polyamines. Full article

(This article belongs to the Special Issue Single-Cell and Single-Molecule Analysis of Microorganism)

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Review

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16 pages, 3337 KiB

Open AccessReview

Single-Molecule/Cell Analyses Reveal Principles of Genome-Folding Mechanisms in the Three Domains of Life

by Hugo Maruyama, Takayuki Nambu, Chiho Mashimo, Toshinori Okinaga and Kunio Takeyasu

Int. J. Mol. Sci. 2021, 22(24), 13432; https://doi.org/10.3390/ijms222413432 - 14 Dec 2021

Viewed by 2822

Abstract

Comparative structural/molecular biology by single-molecule analyses combined with single-cell dissection, mass spectroscopy, and biochemical reconstitution have been powerful tools for elucidating the mechanisms underlying genome DNA folding. All genomes in the three domains of life undergo stepwise folding from DNA to 30–40 nm fibers. Major protein players are histone (Eukarya and Archaea), Alba (Archaea), and HU (Bacteria) for fundamental structural units of the genome. In Euryarchaeota, a major archaeal phylum, either histone or HTa (the bacterial HU homolog) were found to wrap DNA. This finding divides archaea into two groups: those that use DNA-wrapping as the fundamental step in genome folding and those that do not. Archaeal transcription factor-like protein TrmBL2 has been suggested to be involved in genome folding and repression of horizontally acquired genes, similar to bacterial H-NS protein. Evolutionarily divergent SMC proteins contribute to the establishment of higher-order structures. Recent results are presented, including the use of Hi-C technology to reveal that archaeal SMC proteins are involved in higher-order genome folding, and the use of single-molecule tracking to reveal the detailed functions of bacterial and eukaryotic SMC proteins. Here, we highlight the similarities and differences in the DNA-folding mechanisms in the three domains of life. Full article

(This article belongs to the Special Issue Single-Cell and Single-Molecule Analysis of Microorganism)

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