1
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García-Morales A, Balleza D. Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors. J Mol Evol 2023; 91:819-836. [PMID: 37955698 DOI: 10.1007/s00239-023-10140-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023]
Abstract
The voltage-sensing domain (VSD) is a module capable of responding to changes in the membrane potential through conformational changes and facilitating electromechanical coupling to open a pore gate, activate proton permeation pathways, or promote enzymatic activity in some membrane-anchored phosphatases. To carry out these functions, this module acts cooperatively through conformational changes. The VSD is formed by four transmembrane segments (S1-S4) but the S4 segment is critical since it carries positively charged residues, mainly Arg or Lys, which require an aqueous environment for its proper function. The discovery of this module in voltage-gated ion channels (VGICs), proton channels (Hv1), and voltage sensor-containing phosphatases (VSPs) has expanded our understanding of the principle of modularity in the voltage-sensing mechanism of these proteins. Here, by sequence comparison and the evaluation of the relationship between sequence composition, intrinsic flexibility, and structural analysis in 14 selected representatives of these three major protein groups, we report five interesting differences in the folding patterns of the VSD both in prokaryotes and eukaryotes. Our main findings indicate that this module is highly conserved throughout the evolutionary scale, however: (1) segments S1 to S3 in eukaryotes are significantly more hydrophobic than those present in prokaryotes; (2) the S4 segment has retained its hydrophilic character; (3) in eukaryotes the extramembranous linkers are significantly larger and more flexible in comparison with those present in prokaryotes; (4) the sensors present in the kHv1 proton channel and the ciVSP phosphatase, both of eukaryotic origin, exhibit relationships of flexibility and folding patterns very close to the typical ones found in prokaryotic voltage sensors; and (5) archaeal channels KvAP and MVP have flexibility profiles which are clearly contrasting in the S3-S4 region, which could explain their divergent activation mechanisms. Finally, to elucidate the obscure origins of this module, we show further evidence for a possible connection between voltage sensors and TolQ proteins.
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Affiliation(s)
- Abigail García-Morales
- Tecnológico Nacional de México, Instituto Tecnológico de Veracruz, Unidad de Investigación y Desarrollo en Alimentos, Calz. Miguel Angel de Quevedo 2779, Col. Formando Hogar, CP. 91897, Veracruz, Ver, Mexico
| | - Daniel Balleza
- Tecnológico Nacional de México, Instituto Tecnológico de Veracruz, Unidad de Investigación y Desarrollo en Alimentos, Calz. Miguel Angel de Quevedo 2779, Col. Formando Hogar, CP. 91897, Veracruz, Ver, Mexico.
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2
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Ridone P, Ishida T, Lin A, Humphreys DT, Giannoulatou E, Sowa Y, Baker MAB. The rapid evolution of flagellar ion selectivity in experimental populations of E. coli. SCIENCE ADVANCES 2022; 8:eabq2492. [PMID: 36417540 PMCID: PMC9683732 DOI: 10.1126/sciadv.abq2492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Determining which cellular processes facilitate adaptation requires a tractable experimental model where an environmental cue can generate variants that rescue function. The bacterial flagellar motor (BFM) is an excellent candidate-an ancient and highly conserved molecular complex for bacterial propulsion toward favorable environments. Motor rotation is often powered by H+ or Na+ ion transit through the torque-generating stator subunit of the motor complex, and ion selectivity has adapted over evolutionary time scales. Here, we used CRISPR engineering to replace the native Escherichia coli H+-powered stator with Na+-powered stator genes and report the spontaneous reversion of our edit in a low-sodium environment. We followed the evolution of the stators during their reversion to H+-powered motility and used both whole-genome and RNA sequencing to identify genes involved in the cell's adaptation. Our transplant of an unfit protein and the cells' rapid response to this edit demonstrate the adaptability of the stator subunit and highlight the hierarchical modularity of the flagellar motor.
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Affiliation(s)
- Pietro Ridone
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Tsubasa Ishida
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
- Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - David T. Humphreys
- Victor Chang Cardiac Research Institute, Sydney, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Australia
| | | | - Yoshiyuki Sowa
- Department of Frontier Bioscience, Hosei University, Tokyo, Japan
- Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, Australia
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3
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Identification of Genes Required for Swarming Motility in Bacillus subtilis Using Transposon Mutagenesis and High-Throughput Sequencing (TnSeq). J Bacteriol 2022; 204:e0008922. [PMID: 35638827 DOI: 10.1128/jb.00089-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis exhibits swarming motility, a flagellar-mediated form of surface motility. Here, we use transposon mutagenesis and sequencing (TnSeq) to perform a high-throughput screen for candidate genes required for swarming. The TnSeq approach identified all of the known genes required for flagellar biosynthesis and nearly all of the previously reported regulators that promote swarming. Moreover, we identified an additional 36 genes that improve swarming and validated them individually. Among these, two mutants with severe defects were recovered, including fliT, required for flagellar biosynthesis, and a gene of unknown function, yolB, whose defect could not be attributed to a lack of flagella. In addition to discovering additional genes required for B. subtilis swarming, our work validates TnSeq as a powerful approach for comprehensively identifying genes important for nonessential processes such as colony expansion on plates. IMPORTANCE In TnSeq, transposons are randomly inserted throughout the chromosome at a population level, but insertions that disrupt genes of essential function cause strains that carry them to fall out of the population and appear underrepresented at the sequence level. Here, we apply TnSeq to the nonessential phenotype of motility in B. subtilis and spatially select for cells proficient in swarming. We find that insertions in nearly all genes previously identified as required for swarming are underrepresented in TnSeq analysis, and we identify 36 additional genes that enhance swarming. We demonstrate that TnSeq is a powerful tool for the genetic analysis of motility and likely other nonlethal screens for which enrichment is strong.
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4
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MURATA K, KAWAI S, HASHIMOTO W. Bacteria with a mouth: Discovery and new insights into cell surface structure and macromolecule transport. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:529-552. [PMID: 36504195 PMCID: PMC9751261 DOI: 10.2183/pjab.98.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
A bacterium with a "mouth"-like pit structure isolated for the first time in the history of microbiology was a Gram-negative rod, containing glycosphingolipids in the cell envelope, and named Sphingomonas sp. strain A1. The pit was dynamic, with repetitive opening and closing during growth on alginate, and directly included alginate concentrated around the pit, particularly by flagellins, an alginate-binding protein localized on the cell surface. Alginate incorporated into the periplasm was subsequently transferred to the cytoplasm by cooperative interactions of periplasmic solute-binding proteins and an ATP-binding cassette transporter in the cytoplasmic membrane. The mechanisms of assembly, functions, and interactions between the above-mentioned molecules were clarified using structural biology. The pit was transplanted into other strains of sphingomonads, and the pitted recombinant cells were effectively applied to the production of bioethanol, bioremediation for dioxin removal, and other tasks. Studies of the function of the pit shed light on the biological significance of cell surface structures and macromolecule transport in bacteria.
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Affiliation(s)
| | - Shigeyuki KAWAI
- Research Institute for Bioresource and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Wataru HASHIMOTO
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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5
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Matzke NJ, Lin A, Stone M, Baker MAB. Flagellar export apparatus and ATP synthetase: Homology evidenced by synteny predating the Last Universal Common Ancestor. Bioessays 2021; 43:e2100004. [PMID: 33998015 DOI: 10.1002/bies.202100004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 11/07/2022]
Abstract
We report evidence further supporting homology between proteins in the F1 FO -ATP synthetase and the bacterial flagellar motor (BFM). BFM proteins FliH, FliI, and FliJ have been hypothesized to be homologous to FO -b + F1 -δ, F1 -α/β, and F1 -γ, with similar structure and interactions. We conduct a further test by constructing a gene order dataset, examining the order of fliH, fliI, and fliJ genes across the phylogenetic breadth of flagellar and nonflagellar type 3 secretion systems, and comparing this to published surveys of gene order in the F1 FO -ATP synthetase, its N-ATPase relatives, and the bacterial/archaeal V- and A-type ATPases. Strikingly, the fliHIJ gene order was deeply conserved, with the few exceptions appearing derived, and exactly matching the widely conserved F-ATPase gene order atpFHAG, coding for subunits b-δ-α-γ. The V/A-type ATPases have a similar conserved gene order. Our results confirm homology between these systems, and suggest a rare case of synteny conserved over billions of years, predating the Last Universal Common Ancestor (LUCA).
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Affiliation(s)
- Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Micaella Stone
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew A B Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, Australia
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6
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Danowski W, van Leeuwen T, Browne WR, Feringa BL. Photoresponsive porous materials. NANOSCALE ADVANCES 2021; 3:24-40. [PMID: 36131866 PMCID: PMC9417539 DOI: 10.1039/d0na00647e] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/11/2020] [Indexed: 05/04/2023]
Abstract
Molecular machines, switches, and motors enable control over nanoscale molecular motion with unprecedented precision in artificial systems. Integration of these compounds into robust material scaffolds, in particular nanostructured solids, is a fabrication strategy for smart materials with unique properties that can be controlled with external stimuli. Here, we describe a subclass of these structures, namely light-responsive porous materials metal-organic frameworks (MOFs), covalent-organic frameworks (COFs), and porous aromatic frameworks (PAFs) appended with molecular photoswitches. In this review, we provide an overview of a broad range of light-responsive porous materials focusing on potential applications.
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Affiliation(s)
- Wojciech Danowski
- Synthetic Organic Chemistry, Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
| | - Thomas van Leeuwen
- Synthetic Organic Chemistry, Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
| | - Wesley R Browne
- Molecular Inorganic Chemistry, Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
| | - Ben L Feringa
- Synthetic Organic Chemistry, Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 Groningen 9747 AG The Netherlands
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7
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Islam MI, Lin A, Lai YW, Matzke NJ, Baker MAB. Ancestral Sequence Reconstructions of MotB Are Proton-Motile and Require MotA for Motility. Front Microbiol 2020; 11:625837. [PMID: 33424826 PMCID: PMC7787011 DOI: 10.3389/fmicb.2020.625837] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/27/2020] [Indexed: 12/23/2022] Open
Abstract
The bacterial flagellar motor (BFM) is a nanomachine that rotates the flagellum to propel many known bacteria. The BFM is powered by ion transit across the cell membrane through the stator complex, a membrane protein. Different bacteria use various ions to run their BFM, but the majority of BFMs are powered by either proton (H+) or sodium (Na+) ions. The transmembrane (TM) domain of the B-subunit of the stator complex is crucial for ion selectivity, as it forms the ion channel in complex with TM3 and TM4 of the A-subunit. In this study, we reconstructed and engineered thirteen ancestral sequences of the stator B-subunit to evaluate the functional properties and ionic power source of the stator proteins at reconstruction nodes to evaluate the potential of ancestral sequence reconstruction (ASR) methods for stator engineering and to test specific motifs previously hypothesized to be involved in ion-selectivity. We found that all thirteen of our reconstructed ancient B-subunit proteins could assemble into functional stator complexes in combination with the contemporary Escherichia coli MotA-subunit to restore motility in stator deleted E. coli strains. The flagellar rotation of the thirteen ancestral MotBs was found to be Na+ independent which suggested that the F30/Y30 residue was not significantly correlated with sodium/proton phenotype, in contrast to what we had reported previously. Additionally, four among the thirteen reconstructed B-subunits were compatible with the A-subunit of Aquifex aeolicus and able to function in a sodium-independent manner. Overall, this work demonstrates the use of ancestral reconstruction to generate novel stators and quantify which residues are correlated with which ionic power source.
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Affiliation(s)
- Md Imtiazul Islam
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
| | - Angela Lin
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
| | - Yu-Wen Lai
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
| | - Nicholas J. Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences (BABS), University of New South Wales, Sydney, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD, Australia
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8
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Structural Conservation and Adaptation of the Bacterial Flagella Motor. Biomolecules 2020; 10:biom10111492. [PMID: 33138111 PMCID: PMC7693769 DOI: 10.3390/biom10111492] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Many bacteria require flagella for the ability to move, survive, and cause infection. The flagellum is a complex nanomachine that has evolved to increase the fitness of each bacterium to diverse environments. Over several decades, molecular, biochemical, and structural insights into the flagella have led to a comprehensive understanding of the structure and function of this fascinating nanomachine. Notably, X-ray crystallography, cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) have elucidated the flagella and their components to unprecedented resolution, gleaning insights into their structural conservation and adaptation. In this review, we focus on recent structural studies that have led to a mechanistic understanding of flagellar assembly, function, and evolution.
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9
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Wolfson EB, Elvidge J, Tahoun A, Gillespie T, Mantell J, McAteer SP, Rossez Y, Paxton E, Lane F, Shaw DJ, Gill AC, Stevens J, Verkade P, Blocker A, Mahajan A, Gally DL. The interaction of Escherichia coli O157 :H7 and Salmonella Typhimurium flagella with host cell membranes and cytoskeletal components. MICROBIOLOGY (READING, ENGLAND) 2020; 166:947-965. [PMID: 32886602 PMCID: PMC7660914 DOI: 10.1099/mic.0.000959] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022]
Abstract
Bacterial flagella have many established roles beyond swimming motility. Despite clear evidence of flagella-dependent adherence, the specificity of the ligands and mechanisms of binding are still debated. In this study, the molecular basis of Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium flagella binding to epithelial cell cultures was investigated. Flagella interactions with host cell surfaces were intimate and crossed cellular boundaries as demarcated by actin and membrane labelling. Scanning electron microscopy revealed flagella disappearing into cellular surfaces and transmission electron microscopy of S. Typhiumurium indicated host membrane deformation and disruption in proximity to flagella. Motor mutants of E. coli O157:H7 and S. Typhimurium caused reduced haemolysis compared to wild-type, indicating that membrane disruption was in part due to flagella rotation. Flagella from E. coli O157 (H7), EPEC O127 (H6) and S. Typhimurium (P1 and P2 flagella) were shown to bind to purified intracellular components of the actin cytoskeleton and directly increase in vitro actin polymerization rates. We propose that flagella interactions with host cell membranes and cytoskeletal components may help prime intimate attachment and invasion for E. coli O157:H7 and S. Typhimurium, respectively.
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Affiliation(s)
- Eliza B. Wolfson
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Departments of Biochemistry, Biomedical Sciences Building, The University of Bristol, Bristol, BS8 1TD, UK
| | - Johanna Elvidge
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Amin Tahoun
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Faculty of Veterinary Medicine, Kafrelsheikh University, 33516 Kafr el-Sheikh, Egypt
| | - Trudi Gillespie
- IMPACT Facility, Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Judith Mantell
- Departments of Biochemistry, Biomedical Sciences Building, The University of Bristol, Bristol, BS8 1TD, UK
| | - Sean P. McAteer
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Yannick Rossez
- Génie Enzymatique et Cellulaire, UMR 7025 CNRS, Centre de recherche Royallieu, Sorbonne Universités, Université de Technologie de Compiègne, Compiègne Cedex, France
| | - Edith Paxton
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Fiona Lane
- Division of Neurobiology, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Darren J. Shaw
- Division of Clinical Sciences, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Andrew C. Gill
- Division of Neurobiology, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Jo Stevens
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Paul Verkade
- Departments of Biochemistry, Biomedical Sciences Building, The University of Bristol, Bristol, BS8 1TD, UK
| | - Ariel Blocker
- Department of Cellular and Molecular Medicine, Biomedical Sciences Building, The University of Bristol, Bristol, BS8 1TD, UK
| | - Arvind Mahajan
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - David L. Gally
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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10
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Thorvaldsen S, Hössjer O. Using statistical methods to model the fine-tuning of molecular machines and systems. J Theor Biol 2020; 501:110352. [PMID: 32505827 DOI: 10.1016/j.jtbi.2020.110352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 10/24/2022]
Abstract
Fine-tuning has received much attention in physics, and it states that the fundamental constants of physics are finely tuned to precise values for a rich chemistry and life permittance. It has not yet been applied in a broad manner to molecular biology. However, in this paper we argue that biological systems present fine-tuning at different levels, e.g. functional proteins, complex biochemical machines in living cells, and cellular networks. This paper describes molecular fine-tuning, how it can be used in biology, and how it challenges conventional Darwinian thinking. We also discuss the statistical methods underpinning fine-tuning and present a framework for such analysis.
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Affiliation(s)
| | - Ola Hössjer
- Stockholm University, Dep. of Mathematics, Division of Mathematical Statistics, Sweden.
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11
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Miyata M, Robinson RC, Uyeda TQP, Fukumori Y, Fukushima SI, Haruta S, Homma M, Inaba K, Ito M, Kaito C, Kato K, Kenri T, Kinosita Y, Kojima S, Minamino T, Mori H, Nakamura S, Nakane D, Nakayama K, Nishiyama M, Shibata S, Shimabukuro K, Tamakoshi M, Taoka A, Tashiro Y, Tulum I, Wada H, Wakabayashi KI. Tree of motility - A proposed history of motility systems in the tree of life. Genes Cells 2020; 25:6-21. [PMID: 31957229 PMCID: PMC7004002 DOI: 10.1111/gtc.12737] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/17/2019] [Indexed: 12/27/2022]
Abstract
Motility often plays a decisive role in the survival of species. Five systems of motility have been studied in depth: those propelled by bacterial flagella, eukaryotic actin polymerization and the eukaryotic motor proteins myosin, kinesin and dynein. However, many organisms exhibit surprisingly diverse motilities, and advances in genomics, molecular biology and imaging have showed that those motilities have inherently independent mechanisms. This makes defining the breadth of motility nontrivial, because novel motilities may be driven by unknown mechanisms. Here, we classify the known motilities based on the unique classes of movement‐producing protein architectures. Based on this criterion, the current total of independent motility systems stands at 18 types. In this perspective, we discuss these modes of motility relative to the latest phylogenetic Tree of Life and propose a history of motility. During the ~4 billion years since the emergence of life, motility arose in Bacteria with flagella and pili, and in Archaea with archaella. Newer modes of motility became possible in Eukarya with changes to the cell envelope. Presence or absence of a peptidoglycan layer, the acquisition of robust membrane dynamics, the enlargement of cells and environmental opportunities likely provided the context for the (co)evolution of novel types of motility.
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Affiliation(s)
- Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Taro Q P Uyeda
- Department of Physics, Faculty of Science and Technology, Waseda University, Tokyo, Japan
| | - Yoshihiro Fukumori
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Shun-Ichi Fukushima
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Gunma, Japan
| | - Chikara Kaito
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kentaro Kato
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Tsuyoshi Kenri
- Laboratory of Mycoplasmas and Haemophilus, Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Hiroyuki Mori
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shuichi Nakamura
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Miyagi, Japan
| | - Daisuke Nakane
- Department of Physics, Gakushuin University, Tokyo, Japan
| | - Koji Nakayama
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Satoshi Shibata
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Katsuya Shimabukuro
- Department of Chemical and Biological Engineering, National Institute of Technology, Ube College, Yamaguchi, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Azuma Taoka
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Yosuke Tashiro
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Isil Tulum
- Department of Botany, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Hirofumi Wada
- Department of Physics, Graduate School of Science and Engineering, Ritsumeikan University, Shiga, Japan
| | - Ken-Ichi Wakabayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa, Japan
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12
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Feng J, Zong W, Wang P, Zhang ZT, Gu Y, Dougherty M, Borovok I, Wang Y. RRNPP-type quorum-sensing systems regulate solvent formation, sporulation and cell motility in Clostridium saccharoperbutylacetonicum. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:84. [PMID: 32411297 PMCID: PMC7206700 DOI: 10.1186/s13068-020-01723-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Clostridium saccharoperbutylacetonicum N1-4 (HMT) is a strictly anaerobic, spore-forming Gram-positive bacterium capable of hyper-butanol production through the well-known acetone-butanol-ethanol fermentation process. Recently, five putative RRNPP-type QSSs (here designated as QSS1 to QSS5) were predicted in this bacterial strain, each of which comprises a putative RRNPP-type regulator (QssR1 to QssR5) and a cognate signaling peptide precursor (QssP1 to QssP5). In addition, both proteins are encoded by the same operon. The functions of these multiple RRNPP-type QSSs are unknown. RESULTS To elucidate the function of multiple RRNPP-type QSSs as related to cell metabolism and solvent production in N1-4 (HMT), we constructed qssR-deficient mutants ΔR1, ΔR2, ΔR3 and ΔR5 through gene deletion using CRISPR-Cas9 and N1-4-dcas9-R4 (with the QssR4 expression suppressed using CRISPR-dCas9). We also constructed complementation strains by overexpressing the corresponding regulator gene. Based on systematic characterization, results indicate that QSS1, QSS2, QSS3, and QSS5 positively regulate the sol operon expression and thus solvent production, but they likely negatively regulate cell motility. Consequently, QSS4 might not directly regulate solvent production, but positively affect cell migration. In addition, QSS3 and QSS5 appear to positively regulate sporulation efficiency. CONCLUSIONS Our study provides the first insights into the roles of multiple RRNPP-type QSSs of C. saccharoperbutylacetonicum for the regulation of solvent production, cell motility, and sporulation. Results of this study expand our knowledge of how multiple paralogous QSSs are involved in the regulation of essential bacterial metabolism pathways.
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Affiliation(s)
- Jun Feng
- Department of Biosystems Engineering, Auburn University, 350 Mell Street, Auburn, AL 36849 USA
| | - Wenming Zong
- Department of Biosystems Engineering, Auburn University, 350 Mell Street, Auburn, AL 36849 USA
- School of Engineering, Anhui Agricultural University, Hefei, 230036 China
| | - Pixiang Wang
- Department of Biosystems Engineering, Auburn University, 350 Mell Street, Auburn, AL 36849 USA
| | - Zhong-Tian Zhang
- Department of Biosystems Engineering, Auburn University, 350 Mell Street, Auburn, AL 36849 USA
| | - Yanyan Gu
- Department of Biosystems Engineering, Auburn University, 350 Mell Street, Auburn, AL 36849 USA
| | - Mark Dougherty
- Department of Biosystems Engineering, Auburn University, 350 Mell Street, Auburn, AL 36849 USA
| | - Ilya Borovok
- School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 6997801 Tel Aviv, Israel
| | - Yi Wang
- Department of Biosystems Engineering, Auburn University, 350 Mell Street, Auburn, AL 36849 USA
- Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL 36849 USA
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13
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The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries. Trends Microbiol 2020; 28:372-386. [DOI: 10.1016/j.tim.2020.01.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/21/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
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14
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Beeby M, Ferreira JL, Tripp P, Albers SV, Mitchell DR. Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia. FEMS Microbiol Rev 2020; 44:253-304. [DOI: 10.1093/femsre/fuaa006] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
Echoing the repeated convergent evolution of flight and vision in large eukaryotes, propulsive swimming motility has evolved independently in microbes in each of the three domains of life. Filamentous appendages – archaella in Archaea, flagella in Bacteria and cilia in Eukaryotes – wave, whip or rotate to propel microbes, overcoming diffusion and enabling colonization of new environments. The implementations of the three propulsive nanomachines are distinct, however: archaella and flagella rotate, while cilia beat or wave; flagella and cilia assemble at their tips, while archaella assemble at their base; archaella and cilia use ATP for motility, while flagella use ion-motive force. These underlying differences reflect the tinkering required to evolve a molecular machine, in which pre-existing machines in the appropriate contexts were iteratively co-opted for new functions and whose origins are reflected in their resultant mechanisms. Contemporary homologies suggest that archaella evolved from a non-rotary pilus, flagella from a non-rotary appendage or secretion system, and cilia from a passive sensory structure. Here, we review the structure, assembly, mechanism and homologies of the three distinct solutions as a foundation to better understand how propulsive nanomachines evolved three times independently and to highlight principles of molecular evolution.
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Affiliation(s)
- Morgan Beeby
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Josie L Ferreira
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Patrick Tripp
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - David R Mitchell
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 E. Adams St., Syracuse, NY 13210, USA
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15
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Characterization of FliL Proteins in Bradyrhizobium diazoefficiens: Lateral FliL Supports Swimming Motility, and Subpolar FliL Modulates the Lateral Flagellar System. J Bacteriol 2020; 202:JB.00708-19. [PMID: 31843800 DOI: 10.1128/jb.00708-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 12/07/2019] [Indexed: 02/07/2023] Open
Abstract
Bradyrhizobium diazoefficiens is a soil alphaproteobacterium that possesses two evolutionarily distinct flagellar systems, a constitutive subpolar flagellum and inducible lateral flagella that, depending on the carbon source, may be expressed simultaneously in liquid medium and used interactively for swimming. In each system, more than 30 genes encode the flagellar proteins, most of which are well characterized. Among the exceptions is FliL, which has been scarcely studied in alphaproteobacteria and whose function in other bacterial classes is somewhat controversial. Because each B. diazoefficiens flagellar system contains its own fliL paralog, we obtained the respective deletions ΔfliLS (subpolar) and ΔfliLL (lateral) to study their functions in swimming. We determined that FliLL was essential for lateral flagellum-driven motility. FliLS was dispensable for swimming in either liquid or semisolid medium; however, it was found to play a crucial role in upregulation of the lateral flagellum regulon under conditions of increased viscosity/flagellar load. Therefore, although FliLS seems to be not essential for swimming, it may participate in a mechanosensor complex that controls lateral flagellum induction.IMPORTANCE Bacterial motility propelled by flagella is an important trait in most environments, where microorganisms must explore the habitat toward beneficial resources and evade toxins. Most bacterial species have a unique flagellar system, but a few species possess two different flagellar systems in the same cell. An example is Bradyrhizobium diazoefficiens, the N2-fixing symbiont of soybean, which uses both systems for swimming. Among the less-characterized flagellar proteins is FliL, a protein typically associated with a flagellum-driven surface-based collective motion called swarming. By using deletion mutants in each flagellar system's fliL, we observed that one of them (lateral) was required for swimming, while the other (subpolar) took part in the control of lateral flagellum synthesis. Hence, this protein seems to participate in the coordination of activity and production of both flagellar systems.
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16
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Abstract
Bacterial and archaeal flagellins are remarkable in having a shared region with variation in housekeeping proteins and a region with extreme diversity, perhaps greater than for any other protein. Analysis of the 113,285 available full-gene sequences of flagellin genes from published bacterial and archaeal sequences revealed the nature and enormous extent of flagellin diversity. There were 35,898 unique amino acid sequences that were resolved into 187 clusters. Analysis of the Escherichia coli and Salmonella enterica flagellins revealed that the variation occurs at two levels. The first is the division of the variable regions into sequence forms that are so divergent that there is no meaningful alignment even within species, and these corresponded to the E. coli or S. enterica H-antigen groups. The second level is variation within these groups, which is extensive in both species. Shared sequence would allow PCR of the variable regions and thus strain-level analysis of microbiome DNA. Flagellin, the agent of prokaryotic flagellar motion, is very widely distributed and is the H antigen of serology. Flagellin molecules have a variable region that confers serotype specificity, encoded by the middle of the gene, and also conserved regions encoded by the two ends of the gene. We collected all available prokaryotic flagellin protein sequences and found the variable region diversity to be at two levels. In each species investigated, there are hypervariable region (HVR) forms without detectable homology in protein sequences between them. There is also considerable variation within HVR forms, indicating that some have been diverging for thousands of years and that interphylum horizontal gene transfers make a major contribution to the evolution of such atypical diversity. IMPORTANCE Bacterial and archaeal flagellins are remarkable in having a shared region with variation in housekeeping proteins and a region with extreme diversity, perhaps greater than for any other protein. Analysis of the 113,285 available full-gene sequences of flagellin genes from published bacterial and archaeal sequences revealed the nature and enormous extent of flagellin diversity. There were 35,898 unique amino acid sequences that were resolved into 187 clusters. Analysis of the Escherichia coli and Salmonella enterica flagellins revealed that the variation occurs at two levels. The first is the division of the variable regions into sequence forms that are so divergent that there is no meaningful alignment even within species, and these corresponded to the E. coli or S. enterica H-antigen groups. The second level is variation within these groups, which is extensive in both species. Shared sequence would allow PCR of the variable regions and thus strain-level analysis of microbiome DNA.
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17
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Abstract
The bacterial flagellar motor is driven by an ion flux that is converted to torque by motor-attendant complexes known as stators. The dynamics of stator assembly around the motor in response to external stimuli have been the subject of much recent research, but less is known about the evolutionary origins of stator complexes and how they select for specific ions. Here, we review the latest structural and biochemical data for the stator complexes and compare these with other ion transporters and microbial motors to examine possible evolutionary origins of the stator complex.
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18
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19
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Aschtgen MS, Brennan CA, Nikolakakis K, Cohen S, McFall-Ngai M, Ruby EG. Insights into flagellar function and mechanism from the squid-vibrio symbiosis. NPJ Biofilms Microbiomes 2019; 5:32. [PMID: 31666982 PMCID: PMC6814793 DOI: 10.1038/s41522-019-0106-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023] Open
Abstract
Flagella are essential and multifunctional nanomachines that not only move symbionts towards their tissue colonization site, but also play multiple roles in communicating with the host. Thus, untangling the activities of flagella in reaching, interacting, and signaling the host, as well as in biofilm formation and the establishment of a persistent colonization, is a complex problem. The squid-vibrio system offers a unique model to study the many ways that bacterial flagella can influence a beneficial association and, generally, other bacteria-host interactions. Vibrio fischeri is a bioluminescent bacterium that colonizes the Hawaiian bobtail squid, Euprymna scolopes. Over the last 15 years, the structure, assembly, and functions of V. fischeri flagella, including not only motility and chemotaxis, but also biofilm formation and symbiotic signaling, have been revealed. Here we discuss these discoveries in the perspective of other host-bacteria interactions.
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Affiliation(s)
- Marie-Stephanie Aschtgen
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present Address: Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, 171 76 Sweden
| | - Caitlin A. Brennan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present Address: Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Kiel Nikolakakis
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present Address: Department of Natural and Applied Sciences, University of Wisconsin – Green Bay, Green Bay, WI 54311 USA
| | - Stephanie Cohen
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, and Center for Advanced Surface Analysis, Institute of Earth Sciences, Université de Lausanne, CH-1015 Lausanne, Switzerland
- Kewalo Marine Laboratory, University of Hawaii-Manoa, Honolulu, HI 96813 USA
| | | | - Edward G. Ruby
- Kewalo Marine Laboratory, University of Hawaii-Manoa, Honolulu, HI 96813 USA
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20
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Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19 T. Int J Genomics 2019; 2019:7586430. [PMID: 31583244 PMCID: PMC6754898 DOI: 10.1155/2019/7586430] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 11/17/2022] Open
Abstract
Strain E19T described as Hartmannibacter diazotrophicus gen. nov. sp. nov. was isolated from the rhizosphere of Plantago winteri from a natural salt meadow in a nature protection area. Strain E19T is a plant growth-promoting rhizobacterium able to colonize the rhizosphere of barley and to promote its growth only under salt stress conditions. To gain insights into the genetic bases of plant growth promotion and its lifestyle at the rhizosphere under salty conditions, we determined the complete genome sequence using two complementary sequencing platforms (Ilumina MiSeq and PacBio RSII). The E19T genome comprises one circular chromosome and one plasmid containing several genes involved in salt adaptation and genes related to plant growth-promoting traits under salt stress. Based on previous experiments, ACC deaminase activity was identified as a main mechanism of E19T to promote plant growth under salt stress. Interestingly, no genes classically reported to encode for ACC deaminase activity are present. In general, the E19T genome provides information to confirm, discover, and better understand many of its previously evaluated traits involved in plant growth promotion under salt stress. Furthermore, the complete E19T genome sequence helps to define its previously reported unclear 16S rRNA gene-based phylogenetic affiliation. Hartmannibacter forms a distinct subcluster with genera Methylobrevis, Pleomorphomonas, Oharaeibacter, and Mongoliimonas subclustered with genera belonging to Rhizobiales.
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21
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Acharya D, Sullivan MJ, Duell BL, Eveno T, Schembri MA, Ulett GC. Physical Extraction and Fast Protein Liquid Chromatography for Purifying Flagella Filament From Uropathogenic Escherichia coli for Immune Assay. Front Cell Infect Microbiol 2019; 9:118. [PMID: 31069177 PMCID: PMC6491459 DOI: 10.3389/fcimb.2019.00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 04/03/2019] [Indexed: 01/17/2023] Open
Abstract
Flagella are expressed on the surface of a wide range of bacteria, conferring motility and contributing to virulence and innate immune stimulation. Host-pathogen interaction studies of the roles of flagella in infection, including due to uropathogenic Escherichia coli (UPEC), have used various methods to purify and examine the biology of the major flagella subunit protein, FliC. These studies have offered insight into the ways in which flagella proteins interact with host cells. However, previous methods used to extract and purify FliC, such as mechanical shearing, ultracentrifugation, heterologous expression in laboratory E. coli strains, and precipitation-inducing chemical treatments have various limitations; as a result, there are few observations based on highly purified, non-denatured FliC in the literature. This is especially relevant to host-pathogen interaction studies such as immune assays that are designed to parallel, as closely as possible, naturally-occurring interactions between host cells and flagella. In this study, we sought to establish a new, carefully optimized method to extract and purify non-denatured, native FliC from the reference UPEC strain CFT073 to be suitable for immune assays. To achieve purification of FliC to homogeneity, we used a mutant CFT073 strain containing deletions in four major chaperone-usher fimbriae operons (type 1, F1C and two P fimbrial gene clusters; CFT073Δ4). A sequential flagella extraction method based on mechanical shearing, ultracentrifugation, size exclusion chromatography, protein concentration and endotoxin removal was applied to CFT073Δ4. Protein purity and integrity was assessed using SDS-PAGE, Western blots with anti-flagellin antisera, and native-PAGE. We also generated a fliC-deficient strain, CFT073Δ4ΔfliC, to enable the concurrent preparation of a suitable carrier control to be applied in downstream assays. Innate immune stimulation was examined by exposing J774A.1 macrophages to 0.05-1 μg of purified FliC for 5 h; the supernatants were analyzed for cytokines known to be induced by flagella, including TNF-α, IL-6, and IL-12; the results were assessed in the context of prior literature. Macrophage responses to purified FliC encompassed significant levels of several cytokines consistent with prior literature reports. The purification method described here establishes a new approach to examine highly purified FliC in the context of host-pathogen interaction model systems.
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Affiliation(s)
- Dhruba Acharya
- School of Medical Science, Griffith University, Southport, QLD, Australia.,Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Matthew J Sullivan
- School of Medical Science, Griffith University, Southport, QLD, Australia.,Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Benjamin L Duell
- School of Medical Science, Griffith University, Southport, QLD, Australia.,Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Tanguy Eveno
- Institute for Glycomics, Griffith University, Southport, QLD, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Glen C Ulett
- School of Medical Science, Griffith University, Southport, QLD, Australia.,Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
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22
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Ishida T, Ito R, Clark J, Matzke NJ, Sowa Y, Baker MAB. Sodium‐powered stators of the bacterial flagellar motor can generate torque in the presence of phenamil with mutations near the peptidoglycan‐binding region. Mol Microbiol 2019; 111:1689-1699. [DOI: 10.1111/mmi.14246] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Tsubasa Ishida
- Department of Frontier Bioscience Hosei University Tokyo Japan
| | - Rie Ito
- Department of Frontier Bioscience Hosei University Tokyo Japan
| | - Jessica Clark
- School of Biotechnology and Biomolecular Science University of New South Wales Kensington NSW Australia
| | - Nicholas J. Matzke
- School of Biological Sciences University of Auckland Auckland New Zealand
| | - Yoshiyuki Sowa
- Department of Frontier Bioscience Hosei University Tokyo Japan
- Research Center for Micro‐Nano Technology Hosei University Tokyo Japan
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Science University of New South Wales Kensington NSW Australia
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23
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Gordon VD, Wang L. Bacterial mechanosensing: the force will be with you, always. J Cell Sci 2019; 132:132/7/jcs227694. [PMID: 30944157 DOI: 10.1242/jcs.227694] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Whether bacteria are in the planktonic state, free-swimming or free-floating in liquid, or in the biofilm state, sessile on surfaces, they are always subject to mechanical forces. The long, successful evolutionary history of bacteria implies that they are capable of adapting to varied mechanical forces, and probably even actively respond to mechanical cues in their changing environments. However, the sensing of mechanical cues by bacteria, or bacterial mechanosensing, has been under-investigated. This leaves the mechanisms underlying how bacteria perceive and respond to mechanical cues largely unknown. In this Review, we first examine the surface-associated behavior of bacteria, outline the clear evidence for bacterial mechanosensing and summarize the role of flagella, type-IV pili, and envelope proteins as potential mechanosensors, before presenting indirect evidence for mechanosensing in bacteria. The general themes underlying bacterial mechanosensing that we highlight here may provide a framework for future research.
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Affiliation(s)
- Vernita D Gordon
- Department of Physics and Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX 78712, USA .,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Liyun Wang
- Department of Physics and Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, TX 78712, USA
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24
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Bhattacharya S, Baidya AK, Pal RR, Mamou G, Gatt YE, Margalit H, Rosenshine I, Ben-Yehuda S. A Ubiquitous Platform for Bacterial Nanotube Biogenesis. Cell Rep 2019; 27:334-342.e10. [PMID: 30929979 PMCID: PMC6456723 DOI: 10.1016/j.celrep.2019.02.055] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 02/05/2019] [Accepted: 02/13/2019] [Indexed: 01/01/2023] Open
Abstract
We have previously described the existence of membranous nanotubes, bridging adjacent bacteria, facilitating intercellular trafficking of nutrients, cytoplasmic proteins, and even plasmids, yet components enabling their biogenesis remain elusive. Here we reveal the identity of a molecular apparatus providing a platform for nanotube biogenesis. Using Bacillus subtilis (Bs), we demonstrate that conserved components of the flagellar export apparatus (FliO, FliP, FliQ, FliR, FlhB, and FlhA), designated CORE, dually serve for flagellum and nanotube assembly. Mutants lacking CORE genes, but not other flagellar components, are deficient in both nanotube production and the associated intercellular molecular trafficking. In accord, CORE components are located at sites of nanotube emergence. Deleting COREs of distinct species established that CORE-mediated nanotube formation is widespread. Furthermore, exogenous COREs from diverse species could restore nanotube generation and functionality in Bs lacking endogenous CORE. Our results demonstrate that the CORE-derived nanotube is a ubiquitous organelle that facilitates intercellular molecular trade across the bacterial kingdom. Conserved flagellar CORE components dually serve for flagella and nanotube assembly CORE mutants are deficient in nanotube formation and intercellular molecular trade CORE-dependent nanotube production is conserved among distinct bacterial species The CORE-nanotube organelle can provide a common path for bacterial molecular trade
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Affiliation(s)
- Saurabh Bhattacharya
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, POB 12272, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Amit K Baidya
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, POB 12272, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Ritesh Ranjan Pal
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, POB 12272, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Gideon Mamou
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, POB 12272, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Yair E Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, POB 12272, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, POB 12272, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Ilan Rosenshine
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, POB 12272, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel.
| | - Sigal Ben-Yehuda
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, POB 12272, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel.
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25
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Thomson NM, Ferreira JL, Matthews-Palmer TR, Beeby M, Pallen MJ. Giant flagellins form thick flagellar filaments in two species of marine γ-proteobacteria. PLoS One 2018; 13:e0206544. [PMID: 30462661 PMCID: PMC6248924 DOI: 10.1371/journal.pone.0206544] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/15/2018] [Indexed: 01/04/2023] Open
Abstract
Flagella, the primary means of motility in bacteria, are helical filaments that function as microscopic propellers composed of thousands of copies of the protein flagellin. Here, we show that many bacteria encode “giant” flagellins, greater than a thousand amino acids in length, and that two species that encode giant flagellins, the marine γ-proteobacteria Bermanella marisrubri and Oleibacter marinus, produce monopolar flagellar filaments considerably thicker than filaments composed of shorter flagellin monomers. We confirm that the flagellum from B. marisrubri is built from its giant flagellin. Phylogenetic analysis reveals that the mechanism of evolution of giant flagellins has followed a stepwise process involving an internal domain duplication followed by insertion of an additional novel insert. This work illustrates how “the” bacterial flagellum should not be seen as a single, idealised structure, but as a continuum of evolved machines adapted to a range of niches.
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Affiliation(s)
| | - Josie L. Ferreira
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
| | - Mark J. Pallen
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, United Kingdom
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26
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Increased sporulation underpins adaptation of Clostridium difficile strain 630 to a biologically-relevant faecal environment, with implications for pathogenicity. Sci Rep 2018; 8:16691. [PMID: 30420658 PMCID: PMC6232153 DOI: 10.1038/s41598-018-35050-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/24/2018] [Indexed: 02/07/2023] Open
Abstract
Clostridium difficile virulence is driven primarily by the processes of toxinogenesis and sporulation, however many in vitro experimental systems for studying C. difficile physiology have arguably limited relevance to the human colonic environment. We therefore created a more physiologically–relevant model of the colonic milieu to study gut pathogen biology, incorporating human faecal water (FW) into growth media and assessing the physiological effects of this on C. difficile strain 630. We identified a novel set of C. difficile–derived metabolites in culture supernatants, including hexanoyl– and pentanoyl–amino acid derivatives by LC-MSn. Growth of C. difficile strain 630 in FW media resulted in increased cell length without altering growth rate and RNA sequencing identified 889 transcripts as differentially expressed (p < 0.001). Significantly, up to 300–fold increases in the expression of sporulation–associated genes were observed in FW media–grown cells, along with reductions in motility and toxin genes’ expression. Moreover, the expression of classical stress–response genes did not change, showing that C. difficile is well–adapted to this faecal milieu. Using our novel approach we have shown that interaction with FW causes fundamental changes in C. difficile biology that will lead to increased disease transmissibility.
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27
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Hua K, Ferland RJ. Primary cilia proteins: ciliary and extraciliary sites and functions. Cell Mol Life Sci 2018; 75:1521-1540. [PMID: 29305615 PMCID: PMC5899021 DOI: 10.1007/s00018-017-2740-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/21/2017] [Accepted: 12/27/2017] [Indexed: 02/07/2023]
Abstract
Primary cilia are immotile organelles known for their roles in development and cell signaling. Defects in primary cilia result in a range of disorders named ciliopathies. Because this organelle can be found singularly on almost all cell types, its importance extends to most organ systems. As such, elucidating the importance of the primary cilium has attracted researchers from all biological disciplines. As the primary cilia field expands, caution is warranted in attributing biological defects solely to the function of this organelle, since many of these "ciliary" proteins are found at other sites in cells and likely have non-ciliary functions. Indeed, many, if not all, cilia proteins have locations and functions outside the primary cilium. Extraciliary functions are known to include cell cycle regulation, cytoskeletal regulation, and trafficking. Cilia proteins have been observed in the nucleus, at the Golgi apparatus, and even in immune synapses of T cells (interestingly, a non-ciliated cell). Given the abundance of extraciliary sites and functions, it can be difficult to definitively attribute an observed phenotype solely to defective cilia rather than to some defective extraciliary function or a combination of both. Thus, extraciliary sites and functions of cilia proteins need to be considered, as well as experimentally determined. Through such consideration, we will understand the true role of the primary cilium in disease as compared to other cellular processes' influences in mediating disease (or through a combination of both). Here, we review a compilation of known extraciliary sites and functions of "cilia" proteins as a means to demonstrate the potential non-ciliary roles for these proteins.
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Affiliation(s)
- Kiet Hua
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, 47 New Scotland Avenue, MC-136, Albany, NY, 12208, USA.
| | - Russell J Ferland
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, 47 New Scotland Avenue, MC-136, Albany, NY, 12208, USA.
- Department of Neurology, Albany Medical College, Albany, NY, 12208, USA.
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28
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Kong HK, Liu X, Lo WU, Pan Q, Law COK, Chan TF, Ho PL, Lau TCK. Identification of Plasmid-Encoded sRNAs in a blaNDM-1-Harboring Multidrug-Resistance Plasmid pNDM-HK in Enterobacteriaceae. Front Microbiol 2018; 9:532. [PMID: 29636732 PMCID: PMC5880898 DOI: 10.3389/fmicb.2018.00532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/08/2018] [Indexed: 01/15/2023] Open
Abstract
Small RNAs (sRNAs) play significant roles in regulating gene expression post-transcriptionally in response to environmental changes in bacteria. In this work, we identified and characterized six novel sRNAs from an emerging multidrug-resistance (MDR) plasmid pNDM-HK, a New Delhi metallo-β-lactamase 1 gene (blaNDM−1)-carrying IncL/M plasmid that has caused worldwide threat in recent years. These sRNAs are located at different regions of pNDM-HK, such as replication, stability, and variable regions. Moreover, one of the plasmid-encoded sRNAs (NDM-sR3) functions in an Hfq-dependent manner and possibly plays roles in the fitness of pNDM-HK carrying bacteria. In addition, we attempted to construct the phylogenetic tree based on these novel sRNAs and surprisingly, the sRNA-phylogenetic tree provided significant information about the evolutionary pathway of pNDM-HK, including possible gene acquisition and insertion from relevant plasmids. Moreover, the sRNA-phylogenetic tree can specifically cluster the IncM2 type and distinguish it from other IncL/M subtypes. In summary, this is the first study to systematically identify and characterize sRNAs from clinically-isolated MDR plasmids. We believe that these newly found sRNAs could lead to further understanding and new directions to study the evolution and dissemination of the clinically MDR bacterial plasmids.
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Affiliation(s)
- Hoi-Kuan Kong
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Xuan Liu
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Wai U Lo
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Qing Pan
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Carmen O K Law
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Ting F Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Pak L Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Terrence C K Lau
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
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Function and Regulation of Agrobacterium tumefaciens Cell Surface Structures that Promote Attachment. Curr Top Microbiol Immunol 2018; 418:143-184. [PMID: 29998422 DOI: 10.1007/82_2018_96] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Agrobacterium tumefaciens attaches stably to plant host tissues and abiotic surfaces. During pathogenesis, physical attachment to the site of infection is a prerequisite to infection and horizontal gene transfer to the plant. Virulent and avirulent strains may also attach to plant tissue in more benign plant associations, and as with other soil microbes, to soil surfaces in the terrestrial environment. Although most A. tumefaciens virulence functions are encoded on the tumor-inducing plasmid, genes that direct general surface attachment are chromosomally encoded, and thus this process is not obligatorily tied to virulence, but is a more fundamental capacity. Several different cellular structures are known or suspected to contribute to the attachment process. The flagella influence surface attachment primarily via their propulsive activity, but control of their rotation during the transition to the attached state may be quite complex. A. tumefaciens produces several pili, including the Tad-type Ctp pili, and several plasmid-borne conjugal pili encoded by the Ti and At plasmids, as well as the so-called T-pilus, involved in interkingdom horizontal gene transfer. The Ctp pili promote reversible interactions with surfaces, whereas the conjugal and T-pili drive horizontal gene transfer (HGT) interactions with other cells and tissues. The T-pilus is likely to contribute to physical association with plant tissues during DNA transfer to plants. A. tumefaciens can synthesize a variety of polysaccharides including cellulose, curdlan (β-1,3 glucan), β-1,2 glucan (cyclic and linear), succinoglycan, and a localized polysaccharide(s) that is confined to a single cellular pole and is called the unipolar polysaccharide (UPP). Lipopolysaccharides are also in the outer leaflet of the outer membrane. Cellulose and curdlan production can influence attachment under certain conditions. The UPP is required for stable attachment under a range of conditions and on abiotic and biotic surfaces. Other factors that have been reported to play a role in attachment include the elusive protein called rhicadhesin. The process of surface attachment is under extensive regulatory control and can be modulated by environmental conditions, as well as by direct responses to surface contact. Complex transcriptional and post-transcriptional control circuitry underlies much of the production and deployment of these attachment functions.
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Terashima H, Kawamoto A, Morimoto YV, Imada K, Minamino T. Structural differences in the bacterial flagellar motor among bacterial species. Biophys Physicobiol 2017; 14:191-198. [PMID: 29362704 PMCID: PMC5774414 DOI: 10.2142/biophysico.14.0_191] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/19/2017] [Indexed: 12/11/2022] Open
Abstract
The bacterial flagellum is a supramolecular motility machine consisting of the basal body as a rotary motor, the hook as a universal joint, and the filament as a helical propeller. Intact structures of the bacterial flagella have been observed for different bacterial species by electron cryotomography and subtomogram averaging. The core structures of the basal body consisting of the C ring, the MS ring, the rod and the protein export apparatus, and their organization are well conserved, but novel and divergent structures have also been visualized to surround the conserved structure of the basal body. This suggests that the flagellar motors have adapted to function in various environments where bacteria live and survive. In this review, we will summarize our current findings on the divergent structures of the bacterial flagellar motor.
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Affiliation(s)
- Hiroyuki Terashima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yusuke V Morimoto
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
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31
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Abstract
In this issue of Structure, Lynch et al. (2017) reveal that the interaction between two key proteins in the bacterial flagellar motor results in a shared structural domain. This unusual arrangement keeps the corresponding genes together through the course of evolution.
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Affiliation(s)
- Igor B Zhulin
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.
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32
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Pál C, Papp B. Evolution of complex adaptations in molecular systems. Nat Ecol Evol 2017; 1:1084-1092. [PMID: 28782044 PMCID: PMC5540182 DOI: 10.1038/s41559-017-0228-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 05/02/2017] [Indexed: 12/31/2022]
Abstract
A central challenge in evolutionary biology concerns the mechanisms by which complex adaptations arise. Such adaptations depend on the fixation of multiple, highly specific mutations, where intermediate stages of evolution seemingly provide little or no benefit. It is generally assumed that the establishment of complex adaptations is very slow in nature, as evolution of such traits demands special population genetic or environmental circumstances. However, blueprints of complex adaptations in molecular systems are pervasive, indicating that they can readily evolve. We discuss the prospects and limitations of non-adaptive scenarios, which assume multiple neutral or deleterious steps in the evolution of complex adaptations. Next, we examine how complex adaptations can evolve by natural selection in changing environment. Finally, we argue that molecular 'springboards', such as phenotypic heterogeneity and promiscuous interactions facilitate this process by providing access to new adaptive paths.
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Affiliation(s)
- Csaba Pál
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary.
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary
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Štacko P, Kistemaker JCM, Feringa BL. Fluorine-Substituted Molecular Motors with a Quaternary Stereogenic Center. Chemistry 2017; 23:6643-6653. [DOI: 10.1002/chem.201700581] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Peter Štacko
- Centre for Systems Chemistry, Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Jos C. M. Kistemaker
- Centre for Systems Chemistry, Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ben L. Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
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34
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Soo RM, Skennerton CT, Sekiguchi Y, Imelfort M, Paech SJ, Dennis PG, Steen JA, Parks DH, Tyson GW, Hugenholtz P. An expanded genomic representation of the phylum cyanobacteria. Genome Biol Evol 2016; 6:1031-45. [PMID: 24709563 PMCID: PMC4040986 DOI: 10.1093/gbe/evu073] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a nonphotosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of population genomes from human gut and groundwater samples. Here, we expand the phylogenomic representation of the Melainabacteria through sequencing of six diverse population genomes from gut and bioreactor samples supporting the inference that this lineage is nonphotosynthetic, but not the assertion that they are strictly fermentative. We propose that the Melainabacteria is a class within the phylogenetically defined Cyanobacteria based on robust monophyly and shared ancestral traits with photosynthetic representatives. Our findings are consistent with theories that photosynthesis occurred late in the Cyanobacteria and involved extensive lateral gene transfer and extends the recognized functionality of members of this phylum.
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Affiliation(s)
- Rochelle M. Soo
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Connor T. Skennerton
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland, Australia
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Michael Imelfort
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Samuel J. Paech
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Paul G. Dennis
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Present address: School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Jason A. Steen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Donovan H. Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
- *Corresponding author: E-mail:
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35
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Staying in Shape: the Impact of Cell Shape on Bacterial Survival in Diverse Environments. Microbiol Mol Biol Rev 2016; 80:187-203. [PMID: 26864431 DOI: 10.1128/mmbr.00031-15] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacteria display an abundance of cellular forms and can change shape during their life cycle. Many plausible models regarding the functional significance of cell morphology have emerged. A greater understanding of the genetic programs underpinning morphological variation in diverse bacterial groups, combined with assays of bacteria under conditions that mimic their varied natural environments, from flowing freshwater streams to diverse human body sites, provides new opportunities to probe the functional significance of cell shape. Here we explore shape diversity among bacteria, at the levels of cell geometry, size, and surface appendages (both placement and number), as it relates to survival in diverse environments. Cell shape in most bacteria is determined by the cell wall. A major challenge in this field has been deconvoluting the effects of differences in the chemical properties of the cell wall and the resulting cell shape perturbations on observed fitness changes. Still, such studies have begun to reveal the selective pressures that drive the diverse forms (or cell wall compositions) observed in mammalian pathogens and bacteria more generally, including efficient adherence to biotic and abiotic surfaces, survival under low-nutrient or stressful conditions, evasion of mammalian complement deposition, efficient dispersal through mucous barriers and tissues, and efficient nutrient acquisition.
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36
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An evolutionary link between capsular biogenesis and surface motility in bacteria. Nat Rev Microbiol 2015; 13:318-26. [PMID: 25895941 DOI: 10.1038/nrmicro3431] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Studying the evolution of macromolecular assemblies is important to improve our understanding of how complex cellular structures evolved, and to identify the functional building blocks that are involved. Recent studies suggest that the macromolecular complexes that are involved in two distinct processes in Myxococcus xanthus - surface motility and sporulation - are derived from an ancestral polysaccharide capsule assembly system. In this Opinion article, we argue that the available data suggest that the motility machinery evolved from this capsule assembly system following a gene duplication event, a change in carbohydrate polymer specificity and the acquisition of additional proteins by the motility complex, all of which are key features that distinguish the motility and sporulation systems. Furthermore, the presence of intermediates of these systems in bacterial genomes suggests a testable evolutionary model for their emergence and spread.
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37
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Dohra H, Tanaka K, Suzuki T, Fujishima M, Suzuki H. Draft genome sequences of three Holospora species (Holospora obtusa, Holospora undulata, and Holospora elegans), endonuclear symbiotic bacteria of the ciliate Paramecium caudatum. FEMS Microbiol Lett 2015; 359:16-8. [PMID: 25115770 DOI: 10.1111/1574-6968.12577] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/03/2014] [Accepted: 08/07/2014] [Indexed: 11/29/2022] Open
Abstract
We present draft genome sequences of three Holospora species, hosted by the ciliate Paramecium caudatum; that is, the macronucleus-specific H. obtusa and the micronucleus-specific H. undulata and H. elegans. We investigate functions of orthologous core genes conserved across the three Holospora species, which may be essential for the infection and survival in the host nucleus.
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38
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Gao B, Lara-Tejero M, Lefebre M, Goodman AL, Galán JE. Novel components of the flagellar system in epsilonproteobacteria. mBio 2014; 5:e01349-14. [PMID: 24961693 PMCID: PMC4073491 DOI: 10.1128/mbio.01349-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 06/02/2014] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Motility is essential for the pathogenesis of many bacterial species. Most bacteria move using flagella, which are multiprotein filaments that rotate propelled by a cell wall-anchored motor using chemical energy. Although some components of the flagellar apparatus are common to many bacterial species, recent studies have shown significant differences in the flagellar structures of different bacterial species. The molecular bases for these differences, however, are not understood. The flagella from epsilonproteobacteria, which include the bacterial pathogens Campylobacter jejuni and Helicobacter pylori, are among the most divergent. Using next-generation sequencing combined with transposon mutagenesis, we have conducted a comprehensive high-throughput genetic screen in Campylobacter jejuni, which identified several novel components of its flagellar system. Biochemical analyses detected interactions between the identified proteins and known components of the flagellar machinery, and in vivo imaging located them to the bacterial poles, where flagella assemble. Most of the identified new components are conserved within but restricted to epsilonproteobacteria. These studies provide insight into the divergent flagella of this group of bacteria and highlight the complexity of this remarkable structure, which has adapted to carry out its conserved functions in the context of widely diverse bacterial species. IMPORTANCE Motility is essential for the normal physiology and pathogenesis of many bacterial species. Most bacteria move using flagella, which are multiprotein filaments that rotate propelled by a motor that uses chemical energy as fuel. Although some components of the flagellar apparatus are common to many bacterial species, recent studies have shown significant divergence in the flagellar structures across bacterial species. However, the molecular bases for these differences are not understood. The flagella from epsilonproteobacteria, which include the bacterial pathogens Campylobacter jejuni and Helicobacter pylori, are among the most divergent. We conducted a comprehensive genetic screen in Campylobacter jejuni and identified several novel components of the flagellar system. These studies provide important information to understand how flagella have adapted to function in the context of widely diverse sets of bacterial species and bring unique insight into the evolution and function of this remarkable bacterial organelle.
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Affiliation(s)
- Beile Gao
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Maria Lara-Tejero
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Matthew Lefebre
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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39
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Miyazaki R, Bertelli C, Benaglio P, Canton J, De Coi N, Gharib WH, Gjoksi B, Goesmann A, Greub G, Harshman K, Linke B, Mikulic J, Mueller L, Nicolas D, Robinson-Rechavi M, Rivolta C, Roggo C, Roy S, Sentchilo V, Siebenthal AV, Falquet L, van der Meer JR. Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environ Microbiol 2014; 17:91-104. [PMID: 24803113 DOI: 10.1111/1462-2920.12498] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 04/28/2014] [Indexed: 01/24/2023]
Abstract
Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability.
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Affiliation(s)
- Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan; Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
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40
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Doerges L, Kutschera U. Assembly and loss of the polar flagellum in plant-associated methylobacteria. Naturwissenschaften 2014; 101:339-46. [PMID: 24566997 DOI: 10.1007/s00114-014-1162-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/10/2014] [Accepted: 02/12/2014] [Indexed: 01/14/2023]
Abstract
On the leaf surfaces of numerous plant species, inclusive of sunflower (Helianthus annuus L.), pink-pigmented, methanol-consuming, phytohormone-secreting prokaryotes of the genus Methylobacterium have been detected. However, neither the roles, nor the exact mode of colonization of these epiphytic microbes have been explored in detail. Using germ-free sunflower seeds, we document that, during the first days of seedling development, methylobacteria exert no promotive effect on organ growth. Since the microbes are evenly distributed over the outer surface of the above-ground phytosphere, we analyzed the behavior of populations taken from two bacterial strains that were cultivated as solid, biofilm-like clones on agar plates in different aqueous environments (Methylobacterium mesophilicum and M. marchantiae, respectively). After transfer into liquid medium, the rod-shaped, immobile methylobacteria assembled a flagellum and developed into planktonic microbes that were motile. During the linear phase of microbial growth in liquid cultures, the percentage of swimming, flagellated bacteria reached a maximum, and thereafter declined. In stationary populations, living, immotile bacteria, and isolated flagella were observed. Hence, methylobacteria that live in a biofilm, transferred into aqueous environments, assemble a flagellum that is lost when cell density has reached a maximum. This swimming motility, which appeared during ontogenetic development within growing microbial populations, may be a means to colonize the moist outer surfaces of leaves.
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Affiliation(s)
- L Doerges
- Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, 34123, Kassel, Germany
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41
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Theriot JA. Why are bacteria different from eukaryotes? BMC Biol 2013; 11:119. [PMID: 24330667 PMCID: PMC3874686 DOI: 10.1186/1741-7007-11-119] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 12/09/2013] [Indexed: 01/09/2023] Open
Affiliation(s)
- Julie A Theriot
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
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42
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Abstract
This paper presents a heuristic proof (and simulations of a primordial soup) suggesting that life-or biological self-organization-is an inevitable and emergent property of any (ergodic) random dynamical system that possesses a Markov blanket. This conclusion is based on the following arguments: if the coupling among an ensemble of dynamical systems is mediated by short-range forces, then the states of remote systems must be conditionally independent. These independencies induce a Markov blanket that separates internal and external states in a statistical sense. The existence of a Markov blanket means that internal states will appear to minimize a free energy functional of the states of their Markov blanket. Crucially, this is the same quantity that is optimized in Bayesian inference. Therefore, the internal states (and their blanket) will appear to engage in active Bayesian inference. In other words, they will appear to model-and act on-their world to preserve their functional and structural integrity, leading to homoeostasis and a simple form of autopoiesis.
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Affiliation(s)
- Karl Friston
- The Wellcome Trust Centre for Neuroimaging, Institute of Neurology, Queen Square, London WC1N 3BG, UK.
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43
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Allying with armored snails: the complete genome of gammaproteobacterial endosymbiont. ISME JOURNAL 2013; 8:40-51. [PMID: 23924784 DOI: 10.1038/ismej.2013.131] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 06/26/2013] [Accepted: 07/01/2013] [Indexed: 01/12/2023]
Abstract
Deep-sea vents harbor dense populations of various animals that have their specific symbiotic bacteria. Scaly-foot gastropods, which are snails with mineralized scales covering the sides of its foot, have a gammaproteobacterial endosymbiont in their enlarged esophageal glands and diverse epibionts on the surface of their scales. In this study, we report the complete genome sequencing of gammaproteobacterial endosymbiont. The endosymbiont genome displays features consistent with ongoing genome reduction such as large proportions of pseudogenes and insertion elements. The genome encodes functions commonly found in deep-sea vent chemoautotrophs such as sulfur oxidation and carbon fixation. Stable carbon isotope ((13)C)-labeling experiments confirmed the endosymbiont chemoautotrophy. The genome also includes an intact hydrogenase gene cluster that potentially has been horizontally transferred from phylogenetically distant bacteria. Notable findings include the presence and transcription of genes for flagellar assembly, through which proteins are potentially exported from bacterium to the host. Symbionts of snail individuals exhibited extreme genetic homogeneity, showing only two synonymous changes in 19 different genes (13 810 positions in total) determined for 32 individual gastropods collected from a single colony at one time. The extremely low genetic individuality in endosymbionts probably reflects that the stringent symbiont selection by host prevents the random genetic drift in the small population of horizontally transmitted symbiont. This study is the first complete genome analysis of gastropod endosymbiont and offers an opportunity to study genome evolution in a recently evolved endosymbiont.
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Neville BA, Sheridan PO, Harris HMB, Coughlan S, Flint HJ, Duncan SH, Jeffery IB, Claesson MJ, Ross RP, Scott KP, O'Toole PW. Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans. PLoS One 2013; 8:e68919. [PMID: 23935906 PMCID: PMC3720852 DOI: 10.1371/journal.pone.0068919] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 06/03/2013] [Indexed: 02/06/2023] Open
Abstract
Some Eubacterium and Roseburia species are among the most prevalent motile bacteria present in the intestinal microbiota of healthy adults. These flagellate species contribute “cell motility” category genes to the intestinal microbiome and flagellin proteins to the intestinal proteome. We reviewed and revised the annotation of motility genes in the genomes of six Eubacterium and Roseburia species that occur in the human intestinal microbiota and examined their respective locus organization by comparative genomics. Motility gene order was generally conserved across these loci. Five of these species harbored multiple genes for predicted flagellins. Flagellin proteins were isolated from R. inulinivorans strain A2-194 and from E. rectale strains A1-86 and M104/1. The amino-termini sequences of the R. inulinivorans and E. rectale A1-86 proteins were almost identical. These protein preparations stimulated secretion of interleukin-8 (IL-8) from human intestinal epithelial cell lines, suggesting that these flagellins were pro-inflammatory. Flagellins from the other four species were predicted to be pro-inflammatory on the basis of alignment to the consensus sequence of pro-inflammatory flagellins from the β- and γ- proteobacteria. Many fliC genes were deduced to be under the control of σ28. The relative abundance of the target Eubacterium and Roseburia species varied across shotgun metagenomes from 27 elderly individuals. Genes involved in the flagellum biogenesis pathways of these species were variably abundant in these metagenomes, suggesting that the current depth of coverage used for metagenomic sequencing (3.13–4.79 Gb total sequence in our study) insufficiently captures the functional diversity of genomes present at low (≤1%) relative abundance. E. rectale and R. inulinivorans thus appear to synthesize complex flagella composed of flagellin proteins that stimulate IL-8 production. A greater depth of sequencing, improved evenness of sequencing and improved metagenome assembly from short reads will be required to facilitate in silico analyses of complete complex biochemical pathways for low-abundance target species from shotgun metagenomes.
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Affiliation(s)
- B. Anne Neville
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Paul O. Sheridan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, United Kingdom
| | | | - Simone Coughlan
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Harry J. Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, United Kingdom
| | - Sylvia H. Duncan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, United Kingdom
| | - Ian B. Jeffery
- Department of Microbiology, University College Cork, Cork, Ireland
| | | | - R. Paul Ross
- Teagasc Moorepark Food Research Centre, Fermoy, County Cork, Ireland
| | - Karen P. Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, United Kingdom
| | - Paul W. O'Toole
- Department of Microbiology, University College Cork, Cork, Ireland
- * E-mail:
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Elucidating the origin of the ExbBD components of the TonB system through Bayesian inference and maximum-likelihood phylogenies. Mol Phylogenet Evol 2013; 69:674-86. [PMID: 23891663 DOI: 10.1016/j.ympev.2013.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 06/28/2013] [Accepted: 07/12/2013] [Indexed: 01/03/2023]
Abstract
Uptake of ferric siderophores, vitamin B12, and other molecules in gram-negative bacteria is mediated by a multi-protein complex known as the TonB system. The ExbB and ExbD protein components of the TonB system play key energizing roles and are homologous with the flagellar motor proteins MotA and MotB. Here, the phylogenetic relationships of ExbBD and MotAB were investigated using Bayesian inference and the maximum-likelihood method. Phylogenetic trees of these proteins suggest that they are separated into distinct monophyletic groups and have originated from a common ancestral system. Several horizontal gene transfer events for ExbB-ExbD are also inferred, and a model for the evolution of the TonB system is proposed.
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Finster KW, Kjeldsen KU, Kube M, Reinhardt R, Mussmann M, Amann R, Schreiber L. Complete genome sequence of Desulfocapsa sulfexigens, a marine deltaproteobacterium specialized in disproportionating inorganic sulfur compounds. Stand Genomic Sci 2013; 8:58-68. [PMID: 23961312 PMCID: PMC3739170 DOI: 10.4056/sigs.3777412] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Desulfocapsa sulfexigens SB164P1 (DSM 10523) belongs to the deltaproteobacterial family Desulfobulbaceae and is one of two validly described members of its genus. This strain was selected for genome sequencing, because it is the first marine bacterium reported to thrive on the disproportionation of elemental sulfur, a process with a unresolved enzymatic pathway in which elemental sulfur serves both as electron donor and electron acceptor. Furthermore, in contrast to its phylogenetically closest relatives, which are dissimilatory sulfate-reducers, D. sulfexigens is unable to grow by sulfate reduction and appears metabolically specialized in growing by disproportionating elemental sulfur, sulfite or thiosulfate with CO2 as the sole carbon source. The genome of D. sulfexigens contains the set of genes that is required for nitrogen fixation. In an acetylene assay it could be shown that the strain reduces acetylene to ethylene, which is indicative for N-fixation. The circular chromosome of D. sulfexigens SB164P1 comprises 3,986,761 bp and harbors 3,551 protein-coding genes of which 78% have a predicted function based on auto-annotation. The chromosome furthermore encodes 46 tRNA genes and 3 rRNA operons.
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Affiliation(s)
- Kai Waldemar Finster
- Bioscience-Microbiology Section, Aarhus University, Ny Munkegade 116, Dk-8000 Aarhus C, Denmark
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Brigandt I. Intelligent Design and the Nature of Science: Philosophical and Pedagogical Points. THE PHILOSOPHY OF BIOLOGY 2013. [DOI: 10.1007/978-94-007-6537-5_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Abby SS, Rocha EPC. The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems. PLoS Genet 2012; 8:e1002983. [PMID: 23028376 PMCID: PMC3459982 DOI: 10.1371/journal.pgen.1002983] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 08/09/2012] [Indexed: 12/20/2022] Open
Abstract
Type 3 secretion systems (T3SSs) are essential components of two complex bacterial machineries: the flagellum, which drives cell motility, and the non-flagellar T3SS (NF-T3SS), which delivers effectors into eukaryotic cells. Yet the origin, specialization, and diversification of these machineries remained unclear. We developed computational tools to identify homologous components of the two systems and to discriminate between them. Our analysis of >1,000 genomes identified 921 T3SSs, including 222 NF-T3SSs. Phylogenomic and comparative analyses of these systems argue that the NF-T3SS arose from an exaptation of the flagellum, i.e. the recruitment of part of the flagellum structure for the evolution of the new protein delivery function. This reconstructed chronology of the exaptation process proceeded in at least two steps. An intermediate ancestral form of NF-T3SS, whose descendants still exist in Myxococcales, lacked elements that are essential for motility and included a subset of NF-T3SS features. We argue that this ancestral version was involved in protein translocation. A second major step in the evolution of NF-T3SSs occurred via recruitment of secretins to the NF-T3SS, an event that occurred at least three times from different systems. In rhizobiales, a partial homologous gene replacement of the secretin resulted in two genes of complementary function. Acquisition of a secretin was followed by the rapid adaptation of the resulting NF-T3SSs to multiple, distinct eukaryotic cell envelopes where they became key in parasitic and mutualistic associations between prokaryotes and eukaryotes. Our work elucidates major steps of the evolutionary scenario leading to extant NF-T3SSs. It demonstrates how molecular evolution can convert one complex molecular machine into a second, equally complex machine by successive deletions, innovations, and recruitment from other molecular systems.
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Affiliation(s)
- Sophie S Abby
- Département Génomes et Génétique, Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.
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Finnigan GC, Hanson-Smith V, Stevens TH, Thornton JW. Evolution of increased complexity in a molecular machine. Nature 2012; 481:360-4. [PMID: 22230956 DOI: 10.1038/nature10724] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 11/21/2011] [Indexed: 11/09/2022]
Abstract
Many cellular processes are carried out by molecular 'machines'-assemblies of multiple differentiated proteins that physically interact to execute biological functions. Despite much speculation, strong evidence of the mechanisms by which these assemblies evolved is lacking. Here we use ancestral gene resurrection and manipulative genetic experiments to determine how the complexity of an essential molecular machine--the hexameric transmembrane ring of the eukaryotic V-ATPase proton pump--increased hundreds of millions of years ago. We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. Reintroducing a single historical mutation from each paralogue lineage into the resurrected ancestral proteins is sufficient to recapitulate their asymmetric degeneration and trigger the requirement for the more elaborate three-component ring. Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.
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Affiliation(s)
- Gregory C Finnigan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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Muyzer G, Sorokin DY, Mavromatis K, Lapidus A, Foster B, Sun H, Ivanova N, Pati A, D'haeseleer P, Woyke T, Kyrpides NC. Complete genome sequence of Thioalkalivibrio sp. K90mix. Stand Genomic Sci 2011; 5:341-55. [PMID: 22675584 PMCID: PMC3368412 DOI: 10.4056/sigs.2315092] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic sulfur-oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the Gammaproteobacteria. The strain was isolated from a mixture of sediment samples obtained from different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme potassium carbonate tolerance as an enrichment method. Here we report the complete genome sequence of strain K90mix and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from wastewater and gas streams.
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Affiliation(s)
- Gerard Muyzer
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Dimitry Y. Sorokin
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | | | - Alla Lapidus
- Joint Genome Institute, Walnut Creek, California, USA
| | - Brian Foster
- Joint Genome Institute, Walnut Creek, California, USA
| | - Hui Sun
- Joint Genome Institute, Walnut Creek, California, USA
| | | | - Amrita Pati
- Joint Genome Institute, Walnut Creek, California, USA
| | | | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, California, USA
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