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      Molecular ruler of the attachment organelle in Mycoplasma pneumoniae

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          Abstract

          Length control is a fundamental requirement for molecular architecture. Even small wall-less bacteria have specially developed macro-molecular structures to support their survival. Mycoplasma pneumoniae, a human pathogen, forms a polar extension called an attachment organelle, which mediates cell division, cytadherence, and cell movement at host cell surface. This characteristic ultrastructure has a constant size of 250–300 nm, but its design principle remains unclear. In this study, we constructed several mutants by genetic manipulation to increase or decrease coiled-coil regions of HMW2, a major component protein of 200 kDa aligned in parallel along the cell axis. HMW2-engineered mutants produced both long and short attachment organelles, which we quantified by transmission electron microscopy and fluorescent microscopy with nano-meter precision. This simple design of HMW2 acting as a molecular ruler for the attachment organelle should provide an insight into bacterial cellular organization and its function for their parasitic lifestyles.

          Author summary

          Mycoplasma pneumoniae, a pathogen of “walking pneumonia”, have a membrane protrusion with a precise length of 250–300 nm specially developed to support their parasitic lifestyles. To date, however, there has been no report focusing on the potential length-control mechanisms of this characteristic architecture called an attachment organelle. Here, we found that the coiled-coil domains of the 200-kDa protein HMW2 are aligned in parallel along the cell axis, and acts as a molecular ruler by the assembly into a physical scaffold. The molecular ruler could be engineered by genetic modification to produce both longer and shorter attachment organelle. The analyses of the length-controlled mutant highlight a simple design principle of cellular organization in a small bacterium.

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          Predicting coiled coils from protein sequences.

          The probability that a residue in a protein is part of a coiled-coil structure was assessed by comparison of its flanking sequences with sequences of known coiled-coil proteins. This method was used to delineate coiled-coil domains in otherwise globular proteins, such as the leucine zipper domains in transcriptional regulators, and to predict regions of discontinuity within coiled-coil structures, such as the hinge region in myosin. More than 200 proteins that probably have coiled-coil domains were identified in GenBank, including alpha- and beta-tubulins, flagellins, G protein beta subunits, some bacterial transfer RNA synthetases, and members of the heat shock protein (Hsp70) family.
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            Design and synthesis of a minimal bacterial genome.

            We used whole-genome design and complete chemical synthesis to minimize the 1079-kilobase pair synthetic genome of Mycoplasma mycoides JCVI-syn1.0. An initial design, based on collective knowledge of molecular biology combined with limited transposon mutagenesis data, failed to produce a viable cell. Improved transposon mutagenesis methods revealed a class of quasi-essential genes that are needed for robust growth, explaining the failure of our initial design. Three cycles of design, synthesis, and testing, with retention of quasi-essential genes, produced JCVI-syn3.0 (531 kilobase pairs, 473 genes), which has a genome smaller than that of any autonomously replicating cell found in nature. JCVI-syn3.0 retains almost all genes involved in the synthesis and processing of macromolecules. Unexpectedly, it also contains 149 genes with unknown biological functions. JCVI-syn3.0 is a versatile platform for investigating the core functions of life and for exploring whole-genome design.
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              Muscle structure and theories of contraction.

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: ResourcesRole: Writing – original draftRole: Writing – review & editing
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: Resources
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: ResourcesRole: Writing – original draft
                Role: Conceptualization
                Role: ConceptualizationRole: Funding acquisitionRole: Writing – original draft
                Role: Editor
                Journal
                PLoS Pathog
                PLoS Pathog
                plos
                PLoS Pathogens
                Public Library of Science (San Francisco, CA USA )
                1553-7366
                1553-7374
                10 June 2021
                June 2021
                : 17
                : 6
                : e1009621
                Affiliations
                [1 ] Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Tokyo, Japan
                [2 ] Department of Physics, Gakushuin University, Tokyo, Japan
                [3 ] Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
                University of Massachusetts Medical School, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                [¤a]

                Current address: Department of Bacteriology, Nagoya University Graduate School of Medicine, Japan

                Author information
                https://orcid.org/0000-0002-8201-2608
                https://orcid.org/0000-0002-3198-4263
                https://orcid.org/0000-0002-1233-6842
                Article
                PPATHOGENS-D-21-00329
                10.1371/journal.ppat.1009621
                8191905
                2acf57ce-2dfa-4992-b635-9160de5d4fde
                © 2021 Nakane et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 12 February 2021
                : 7 May 2021
                Page count
                Figures: 5, Tables: 0, Pages: 15
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 15H01329
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 16H06230
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 20H05543
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 21K07020
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 25117530
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 15H01337
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 16H00808
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 15H01218
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 15H04364
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100007684, Asahi Glass Foundation;
                Award Recipient :
                Funded by: Nakajima Foundation
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100004051, Kato Memorial Bioscience Foundation;
                Award Recipient :
                Funded by: Noguchi institute
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100007428, Naito Foundation;
                Award Recipient :
                This study was supported in part by KAKENHI grants from the Japan Society for the Promotion of Science (15H01329, 16H06230, 20H05543, and 21K07020 to D.N., 25117530 and 15H01337 to T.K., and 16H00808, 15H01218, and 15H04364 to T.N.), grants from Japan Agency for Medical Research and Development (20jk0210004j0101) to TK, and by funds from the Asahi Glass Foundation ( https://www.af-info.or.jp/en/) to DN, the Nakajima Foundation ( http://www.nakajimafound.or.jp/) to DN, the Kato Memorial Bioscience Foundation ( https://www.katokinen.or.jp/) to DN, the Noguchi institute ( https://www.noguchi.or.jp/) to DN, and the Naito Foundation ( https://www.naito-f.or.jp/en/) to D.N. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Cytoskeleton
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Bacterial Pathogens
                Mycoplasma Pneumoniae
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Bacterial Pathogens
                Mycoplasma Pneumoniae
                Biology and Life Sciences
                Organisms
                Bacteria
                Mollicutes
                Mycoplasma
                Mycoplasma Pneumoniae
                Biology and Life Sciences
                Biochemistry
                Proteins
                Luminescent Proteins
                Yellow Fluorescent Protein
                Biology and Life Sciences
                Cell Biology
                Cell Motility
                Research and Analysis Methods
                Imaging Techniques
                Fluorescence Imaging
                Research and Analysis Methods
                Microscopy
                Electron Microscopy
                Biology and Life Sciences
                Cell Biology
                Cell Physiology
                Cell Polarity
                Custom metadata
                All relevant data are within the manuscript and its Supporting Information files.

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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