1
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Murphy P, Perepelitsa M, Timofeyev I, Lieber-Kotz M, Islas B, Igoshin OA. Breakdown of Boltzmann-type models for the alignment of self-propelled rods. Math Biosci 2024; 376:109266. [PMID: 39127094 DOI: 10.1016/j.mbs.2024.109266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/23/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024]
Abstract
Studies in the collective motility of organisms use a range of analytical approaches to formulate continuous kinetic models of collective dynamics from rules or equations describing agent interactions. However, the derivation of these kinetic models often relies on Boltzmann's "molecular chaos" hypothesis, which assumes that correlations between individuals are short-lived. While this assumption is often the simplest way to derive tractable models, it is often not valid in practice due to the high levels of cooperation and self-organization present in biological systems. In this work, we illustrated this point by considering a general Boltzmann-type kinetic model for the alignment of self-propelled rods where rod reorientation occurs upon binary collisions. We examine the accuracy of the kinetic model by comparing numerical solutions of the continuous equations to an agent-based model that implements the underlying rules governing microscopic alignment. Even for the simplest case considered, our comparison demonstrates that the kinetic model fails to replicate the discrete dynamics due to the formation of rod clusters that violate statistical independence. Additionally, we show that introducing noise to limit cluster formation helps improve the agreement between the analytical model and agent simulations but does not restore the agreement completely. These results highlight the need to both develop and disseminate improved moment-closure methods for modeling biological and active matter systems.
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Affiliation(s)
- Patrick Murphy
- Department of Mathematics and Statistics, San Jose State University, San Jose, CA 95192, United States of America.
| | - Misha Perepelitsa
- Department of Mathematics, University of Houston, TX 77204, United States of America
| | - Ilya Timofeyev
- Department of Mathematics, University of Houston, TX 77204, United States of America
| | - Matan Lieber-Kotz
- Department of Bioengineering, Rice University, Houston, TX 77005, United States of America
| | - Brandon Islas
- Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, United States of America
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, Houston, TX 77005, United States of America; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States of America; Department of Chemistry, Rice University, Houston, TX 77005, United States of America; Department of Biosciences, Rice University, Houston, TX 77005, United States of America
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2
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Ros-Rocher N. The evolution of multicellularity and cell differentiation symposium: bridging evolutionary cell biology and computational modelling using emerging model systems. Biol Open 2024; 13:bio061720. [PMID: 39373528 DOI: 10.1242/bio.061720] [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: 09/02/2024] [Accepted: 09/09/2024] [Indexed: 10/08/2024] Open
Abstract
'The evolution of multicellularity and cell differentiation' symposium, organized as part of the EuroEvoDevo 2024 meeting on June 25-28th in Helsinki (Finland), addressed recent advances on the molecular and mechanistic basis for the evolution of multicellularity and cell differentiation in eukaryotes. The symposium involved over 100 participants and brought together 10 speakers at diverse career stages. Talks covered various topics at the interface of developmental biology, evolutionary cell biology, comparative genomics, computational biology, and ecology using animal, protist, algal and mathematical models. This symposium offered a unique opportunity for interdisciplinary dialog among researchers working on different systems, especially in promoting collaborations and aligning strategies for studying emerging model species. Moreover, it fostered opportunities to promote early career researchers in the field and opened discussions of ongoing work and unpublished results. In this Meeting Review, we aim to promote the research, capture the spirit of the meeting, and present key topics discussed within this dynamic, growing and open community.
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Affiliation(s)
- Núria Ros-Rocher
- Institut Pasteur, Université Paris-Cité, CNRS UMR3691, Evolutionary Cell Biology and Evolution of Morphogenesis Unit, 25-28 Rue du Dr. Roux, 75015 Paris, France
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3
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Wang CY, Hu JQ, Wang DG, Li YZ, Wu C. Recent advances in discovery and biosynthesis of natural products from myxobacteria: an overview from 2017 to 2023. Nat Prod Rep 2024; 41:905-934. [PMID: 38390645 DOI: 10.1039/d3np00062a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Covering: 2017.01 to 2023.11Natural products biosynthesized by myxobacteria are appealing due to their sophisticated chemical skeletons, remarkable biological activities, and intriguing biosynthetic enzymology. This review aims to systematically summarize the advances in the discovery methods, new structures, and bioactivities of myxobacterial NPs reported in the period of 2017-2023. In addition, the peculiar biosynthetic pathways of several structural families are also highlighted.
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Affiliation(s)
- Chao-Yi Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - De-Gao Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
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4
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Zhu LL, Yang Q, Wang DG, Niu L, Pan Z, Li S, Li YZ, Zhang W, Wu C. Deciphering the Biosynthesis and Physiological Function of 5-Methylated Pyrazinones Produced by Myxobacteria. ACS CENTRAL SCIENCE 2024; 10:555-568. [PMID: 38559311 PMCID: PMC10979478 DOI: 10.1021/acscentsci.3c01363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/25/2023] [Accepted: 01/16/2024] [Indexed: 04/04/2024]
Abstract
Myxobacteria are a prolific source of secondary metabolites with sheer chemical complexity, intriguing biosynthetic enzymology, and diverse biological activities. In this study, we report the discovery, biosynthesis, biomimetic total synthesis, physiological function, structure-activity relationship, and self-resistance mechanism of the 5-methylated pyrazinone coralinone from a myxobacterium Corallococcus exiguus SDU70. A single NRPS/PKS gene corA was genetically and biochemically demonstrated to orchestrate coralinone, wherein the integral PKS part is responsible for installing the 5-methyl group. Intriguingly, coralinone exacerbated cellular aggregation of myxobacteria grown in liquid cultures by enhancing the secretion of extracellular matrix, and the 5-methylation is indispensable for the alleged activity. We provided an evolutionary landscape of the corA-associated biosynthetic gene clusters (BGCs) distributed in the myxobacterial realm, revealing the divergent evolution for the diversity-oriented biosynthesis of 5-alkyated pyrazinones. This phylogenetic contextualization provoked us to identify corB located in the proximity of corA as a self-resistance gene. CorB was experimentally verified to be a protease that hydrolyzes extracellular proteins to antagonize the agglutination-inducing effect of coralinone. Overall, we anticipate these findings will provide new insights into the chemical ecology of myxobacteria and lay foundations for the maximal excavation of these largely underexplored resources.
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Affiliation(s)
| | | | | | - Luo Niu
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Zhuo Pan
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Shengying Li
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Wei Zhang
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
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5
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Zang Y, Zhang X, Wang Z, Tong Q, Zhou Y, Yao Q, Zhu H. Hyalangiumruber sp. nov, characterization of a novel myxobacterium strain s54d21 and their secondary metabolites. Front Microbiol 2024; 15:1369499. [PMID: 38525079 PMCID: PMC10959286 DOI: 10.3389/fmicb.2024.1369499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/22/2024] [Indexed: 03/26/2024] Open
Abstract
Myxobacteria are special bacteria with wide adaptability, which are rich sources of structurally diverse natural products with intriguing biological properties. Here, a gram-negative myxobacterium strain s54d21T was isolated from the sediment of a wetland park in China using the Escherichia coli baiting method. Based on 16S rRNA gene sequence and genomic data, the strain was demonstrated to be a novel species of a rare genus Hyalangium, designated Hyalangium ruber sp. nov (type strain s54d21T = GDMCC 1.1945T = JCM 39263T). The subsequent chemical investigation of the strain s54d21T led to the isolation of three rare 3,5,6-trisubstituted 2(1H)-pyrazinones, namely, hyalanones A-C (1-3), together with a known macrolactin A (4). Those new structures and their absolute configurations were unambiguously assigned by extensive analyses of spectroscopic data and density functional theory (DFT) calculations. In biological assays, compound 4 exhibited moderate cytotoxic activities against human cell lines RKO, A549, and NCM460 with IC50 values ranging from 27.21 to 32.14 μM.
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Affiliation(s)
- Yi Zang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xianjiao Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- College of Horticulture, South China Agriculture University, Guangzhou, China
| | - Zhe Wang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingyi Tong
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Zhou
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qing Yao
- College of Horticulture, South China Agriculture University, Guangzhou, China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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6
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Murphy P, Comstock J, Khan T, Zhang J, Welch R, Igoshin OA. Cell behaviors underlying Myxococcus xanthus aggregate dispersal. mSystems 2023; 8:e0042523. [PMID: 37747885 PMCID: PMC10654071 DOI: 10.1128/msystems.00425-23] [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: 05/08/2023] [Accepted: 07/27/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Understanding the processes behind bacterial biofilm formation, maintenance, and dispersal is essential for addressing their effects on health and ecology. Within these multicellular communities, various cues can trigger differentiation into distinct cell types, allowing cells to adapt to their specific local environment. The soil bacterium Myxococcus xanthus forms biofilms in response to starvation, marked by cells aggregating into mounds. Some aggregates persist as spore-filled fruiting bodies, while others disperse after initial formation for unknown reasons. Here, we use a combination of cell tracking analysis and computational simulations to identify behaviors at the cellular level that contribute to aggregate dispersal. Our results suggest that cells in aggregates actively determine whether to disperse or persist and undergo a transition to sporulation based on a self-produced cue related to the aggregate size. Identifying these cues is an important step in understanding and potentially manipulating bacterial cell-fate decisions.
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Affiliation(s)
- Patrick Murphy
- Department of Bioengineering, Rice University, Houston, Texas, USA
- Center for Theoretical Physical Biology, Rice University, Houston, Texas, USA
| | - Jessica Comstock
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Trosporsha Khan
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Jiangguo Zhang
- Department of Bioengineering, Rice University, Houston, Texas, USA
- Center for Theoretical Physical Biology, Rice University, Houston, Texas, USA
| | - Roy Welch
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Oleg A. Igoshin
- Department of Bioengineering, Rice University, Houston, Texas, USA
- Center for Theoretical Physical Biology, Rice University, Houston, Texas, USA
- Department of Chemistry, Rice University, Houston, Texas, USA
- Department of Biosciences, Rice University, Houston, Texas, USA
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7
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Liu L, Xu F, Lei J, Wang P, Zhang L, Wang J, Zhao J, Mao D, Ye X, Huang Y, Hu G, Cui Z, Li Z. Genome analysis of a plasmid-bearing myxobacterim Myxococcus sp. strain MxC21 with salt-tolerant property. Front Microbiol 2023; 14:1250602. [PMID: 37789850 PMCID: PMC10544341 DOI: 10.3389/fmicb.2023.1250602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
Myxobacteria are widely distributed in various habitats of soil and oceanic sediment. However, it is unclear whether soil-dwelling myxobacteria tolerate a saline environment. In this study, a salt-tolerant myxobacterium Myxococcus sp. strain MxC21 was isolated from forest soil with NaCl tolerance >2% concentration. Under 1% salt-contained condition, strain MxC21 could kill and consume bacteria prey and exhibited complex social behaviors such as S-motility, biofilm, and fruiting body formation but adopted an asocial living pattern with the presence of 1.5% NaCl. To investigate the genomic basis of stress tolerance, the complete genome of MxC21 was sequenced and analyzed. Strain MxC21 consists of a circular chromosome with a total length of 9.13 Mbp and a circular plasmid of 64.3 kb. Comparative genomic analysis revealed that the genomes of strain MxC21 and M. xanthus DK1622 share high genome synteny, while no endogenous plasmid was found in DK1622. Further analysis showed that approximately 21% of its coding genes from the genome of strain MxC21 are predominantly associated with signal transduction, transcriptional regulation, and protein folding involved in diverse niche adaptation such as salt tolerance, which enables social behavior such as gliding motility, sporulation, and predation. Meantime, a high number of genes are also found to be involved in defense against oxidative stress and production of antimicrobial compounds. All of these functional genes may be responsible for the potential salt-toleration. Otherwise, strain MxC21 is the second reported myxobacteria containing indigenous plasmid, while only a small proportion of genes was specific to the circular plasmid of strain MxC21, and most of them were annotated as hypothetical proteins, which may have a direct relationship with the habitat adaptation of strain MxC21 under saline environment. This study provides an inspiration of the adaptive evolution of salt-tolerant myxobacterium and facilitates a potential application in the improvement of saline soil in future.
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Affiliation(s)
- Lin Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fengjuan Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jinhui Lei
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Peiwen Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Lei Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jihong Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jingya Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Dongmei Mao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Gang Hu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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8
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Rombouts S, Mas A, Le Gall A, Fiche JB, Mignot T, Nollmann M. Multi-scale dynamic imaging reveals that cooperative motility behaviors promote efficient predation in bacteria. Nat Commun 2023; 14:5588. [PMID: 37696789 PMCID: PMC10495355 DOI: 10.1038/s41467-023-41193-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 08/21/2023] [Indexed: 09/13/2023] Open
Abstract
Many species, such as fish schools or bird flocks, rely on collective motion to forage, prey, or escape predators. Likewise, Myxococcus xanthus forages and moves collectively to prey and feed on other bacterial species. These activities require two distinct motility machines enabling adventurous (A) and social (S) gliding, however when and how these mechanisms are used has remained elusive. Here, we address this long-standing question by applying multiscale semantic cell tracking during predation. We show that: (1) foragers and swarms can comprise A- and S-motile cells, with single cells exchanging frequently between these groups; (2) A-motility is critical to ensure the directional movement of both foragers and swarms; (3) the combined action of A- and S-motile cells within swarms leads to increased predation efficiencies. These results challenge the notion that A- and S-motilities are exclusive to foragers and swarms, and show that these machines act synergistically to enhance predation efficiency.
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Affiliation(s)
- Sara Rombouts
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090, Montpellier, France
| | - Anna Mas
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090, Montpellier, France
| | - Antoine Le Gall
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090, Montpellier, France.
| | - Jean-Bernard Fiche
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090, Montpellier, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, Marseille, France
| | - Marcelo Nollmann
- Centre de Biologie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090, Montpellier, France.
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9
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Wang X, Blumenfeld R, Feng XQ, Weitz DA. 'Phase transitions' in bacteria - From structural transitions in free living bacteria to phenotypic transitions in bacteria within biofilms. Phys Life Rev 2022; 43:98-138. [PMID: 36252408 DOI: 10.1016/j.plrev.2022.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 12/05/2022]
Abstract
Phase transitions are common in inanimate systems and have been studied extensively in natural sciences. Less explored are the rich transitions that take place at the micro- and nano-scales in biological systems. In conventional phase transitions, large-scale properties of the media change discontinuously in response to continuous changes in external conditions. Such changes play a significant role in the dynamic behaviours of organisms. In this review, we focus on some transitions in both free-living and biofilms of bacteria. Particular attention is paid to the transitions in the flagellar motors and filaments of free-living bacteria, in cellular gene expression during the biofilm growth, in the biofilm morphology transitions during biofilm expansion, and in the cell motion pattern transitions during the biofilm formation. We analyse the dynamic characteristics and biophysical mechanisms of these phase transition phenomena and point out the parallels between these transitions and conventional phase transitions. We also discuss the applications of some theoretical and numerical methods, established for conventional phase transitions in inanimate systems, in bacterial biofilms.
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Affiliation(s)
- Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China; John A. Paulson School of Engineering and Applied Sciences, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA.
| | - Raphael Blumenfeld
- Gonville & Caius College, University of Cambridge, Trinity St., Cambridge CB2 1TA, UK
| | - Xi-Qiao Feng
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA; Department of Physics, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA
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10
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Perepelitsa M, Timofeyev I, Murphy P, Igoshin OA. Mean-field model for nematic alignment of self-propelled rods. Phys Rev E 2022; 106:034613. [PMID: 36266908 DOI: 10.1103/physreve.106.034613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Self-propelled rods are a facet of the field of active matter relevant to many physical systems ranging in scale from shaken granular media and bacterial alignment to the flocking dynamics of animals. In this paper we develop a model for nematic alignment of self-propelled rods interacting through binary collisions. We avoid phenomenological descriptions of rod interaction in favor of rigorously using a set of microscopic-level rules. Under the assumption that each collision results in a small change to a rod's orientation, we derive the Fokker-Planck equation for the evolution of the kinetic density function. Using analytical and numerical methods, we study the emergence of the nematic order from a homogeneous, uniform steady state of the mean-field equation. We compare the level of orientational noise needed to destabilize this nematic order and compare our results to an existing phenomenological model that does not explicitly account for the physical collisions of rods. We show the presence of an additional geometric factor in our equations reflecting a reduced collision rate between nearly aligned rods that reduces the level of noise at which nematic order is destroyed, suggesting that alignment that depends on purely physical collisions is less robust.
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Affiliation(s)
| | - Ilya Timofeyev
- Department of Mathematics, University of Houston, Texas 77204, USA
| | - Patrick Murphy
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
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11
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Jose A, Ariel G, Be'er A. Physical characteristics of mixed-species swarming colonies. Phys Rev E 2022; 105:064404. [PMID: 35854624 DOI: 10.1103/physreve.105.064404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
In nature, bacterial collectives typically consist of multiple species, which are interacting both biochemically and physically. Nonetheless, past studies on the physical properties of swarming bacteria were focused on axenic (single-species) populations. In bacterial swarming, intricate interactions between the individuals lead to clusters, rapid jets, and vortices that depend on cell characteristics such as speed and length. In this work, we show the first results of rapidly swarming mixed-species populations of Bacillus subtilis and Serratia marcescens, two model swarm species that are known to swarm well in axenic situations. In mixed liquid cultures, both species have higher reproduction rates. We show that the mixed population swarms together well and that the fraction between the species determines all dynamical scales-from the microscopic (e.g., speed distribution), mesoscopic (vortex size), and macroscopic (colony structure and size). Understanding mixed-species swarms is essential for a comprehensive understanding of the bacterial swarming phenomenon and its biological and evolutionary implications.
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Affiliation(s)
- Ajesh Jose
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Midreshet Ben-Gurion, Israel
| | - Gil Ariel
- Department of Mathematics, Bar-Ilan University, 52000 Ramat Gan, Israel
| | - Avraham Be'er
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Midreshet Ben-Gurion, Israel and Department of Physics, Ben-Gurion University of the Negev 84105, Beer-Sheva, Israel
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12
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Do H, Madukoma CS, Sundaresan V, Shrout JD, Hoffman AJ, Bohn PW. Spatiotemporal distribution of chemical signatures exhibited by Myxococcus xanthus in response to metabolic conditions. Anal Bioanal Chem 2021; 414:1691-1698. [PMID: 34850244 DOI: 10.1007/s00216-021-03795-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 11/25/2022]
Abstract
Myxococcus xanthus is a common soil bacterium with a complex life cycle, which is known for production of secondary metabolites. However, little is known about the effects of nutrient availability on M. xanthus metabolite production. In this study, we utilize confocal Raman microscopy (CRM) to examine the spatiotemporal distribution of chemical signatures secreted by M. xanthus and their response to varied nutrient availability. Ten distinct spectral features are observed by CRM from M. xanthus grown on nutrient-rich medium. However, when M. xanthus is constrained to grow under nutrient-limited conditions, by starving it of casitone, it develops fruiting bodies, and the accompanying Raman microspectra are dramatically altered. The reduced metabolic state engendered by the absence of casitone in the medium is associated with reduced, or completely eliminated, features at 1140 cm-1, 1560 cm-1, and 1648 cm-1. In their place, a feature at 1537 cm-1 is observed, this feature being tentatively assigned to a transitional phase important for cellular adaptation to varying environmental conditions. In addition, correlating principal component analysis heat maps with optical images illustrates how fruiting bodies in the center co-exist with motile cells at the colony edge. While the metabolites responsible for these Raman features are not completely identified, three M. xanthus peaks at 1004, 1151, and 1510 cm-1 are consistent with the production of lycopene. Thus, a combination of CRM imaging and PCA enables the spatial mapping of spectral signatures of secreted factors from M. xanthus and their correlation with metabolic conditions.
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Affiliation(s)
- Hyein Do
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Chinedu S Madukoma
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Vignesh Sundaresan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Anthony J Hoffman
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA. .,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.
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13
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Ramos CH, Rodríguez-Sánchez E, Del Angel JAA, Arzola AV, Benítez M, Escalante AE, Franci A, Volpe G, Rivera-Yoshida N. The environment topography alters the way to multicellularity in Myxococcus xanthus. SCIENCE ADVANCES 2021; 7:7/35/eabh2278. [PMID: 34433567 PMCID: PMC8386931 DOI: 10.1126/sciadv.abh2278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/02/2021] [Indexed: 05/10/2023]
Abstract
The social soil-dwelling bacterium Myxococcus xanthus can form multicellular structures, known as fruiting bodies. Experiments in homogeneous environments have shown that this process is affected by the physicochemical properties of the substrate, but they have largely neglected the role of complex topographies. We experimentally demonstrate that the topography alters single-cell motility and multicellular organization in M. xanthus In topographies realized by randomly placing silica particles over agar plates, we observe that the cells' interaction with particles drastically modifies the dynamics of cellular aggregation, leading to changes in the number, size, and shape of the fruiting bodies and even to arresting their formation in certain conditions. We further explore this type of cell-particle interaction in a computational model. These results provide fundamental insights into how the environment topography influences the emergence of complex multicellular structures from single cells, which is a fundamental problem of biological, ecological, and medical relevance.
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Affiliation(s)
- Corina H Ramos
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. de México, C.P. 4510, Mexico
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Edna Rodríguez-Sánchez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Juan Antonio Arias Del Angel
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Alejandro V Arzola
- Instituto de Física, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, México
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Ana E Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Alessio Franci
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. de México, C.P. 4510, Mexico
| | - Giovanni Volpe
- Department of Physics, University of Gothenburg, Gothenburg, Sweden
| | - Natsuko Rivera-Yoshida
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. de México, C.P. 4510, Mexico.
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
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14
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The evolution of convex trade-offs enables the transition towards multicellularity. Nat Commun 2021; 12:4222. [PMID: 34244514 PMCID: PMC8270964 DOI: 10.1038/s41467-021-24503-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/17/2021] [Indexed: 11/13/2022] Open
Abstract
The evolutionary transition towards multicellular life often involves growth in groups of undifferentiated cells followed by differentiation into soma and germ-like cells. Theory predicts that germ soma differentiation is facilitated by a convex trade-off between survival and reproduction. However, this has never been tested and these transitions remain poorly understood at the ecological and genetic level. Here, we study the evolution of cell groups in ten isogenic lines of the unicellular green algae Chlamydomonas reinhardtii with prolonged exposure to a rotifer predator. We confirm that growth in cell groups is heritable and characterized by a convex trade-off curve between reproduction and survival. Identical mutations evolve in all cell group isolates; these are linked to survival and reducing associated cell costs. Overall, we show that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome. Multicellularity is a major evolutionary transition that remains poorly characterized at the ecological and genetic level. Exposing unicellular green algae to a rotifer predator showed that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.
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15
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Harita D, Kanie K, Kimura Y. Enzymatic properties of Myxococcus xanthus exopolyphosphatases mxPpx1 and mxPpx2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140660. [PMID: 33857634 DOI: 10.1016/j.bbapap.2021.140660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/02/2021] [Accepted: 04/10/2021] [Indexed: 11/18/2022]
Abstract
Myxococcus xanthus possesses two exopolyphosphatases, mxPpx1 and mxPpx2, which belong to the family of Ppx/GppA phosphatases; however, their catalytic properties have not been described. mxPpx1 and mxPpx2 contain 311 and 505 amino acid residues, respectively; mxPpx2 has an additional C-terminal region, which corresponds to the metal-dependent HDc phosphohydrolase domain. mxPpx1 mainly hydrolyzed short-chain polyPs (polyP3 and polyP4), whereas mxPpx2 preferred long-chain polyP60-70 and polyP700-1000. mxPpx2 was activated by 25-50 mM KCl, but mxPpx1 did not significantly depend on K+. In addition, mxPpx1 and mxPpx2 showed weak hydrolysis of ATP and GTP in the absence of K+, and mxPpx2 could also hydrolyze guanosine pentaphosphate (pppGpp) in the presence of K+. The exopolyphosphatase activity of mxPpx1 toward polyP3 was inhibited by polyP700-1000 and that of mxPpx2 toward polyP60-70 and polyP700-1000, by pyrophosphate. To clarify the function of the mxPpx2 C-terminal domain, it was fused to mxPpx1 (mxPpx1-2C) and deleted from mxPpx2 (mxPpx2∆C). Compared to wild-type mxPpx2, mxPpx2∆C had significantly reduced exopolyphosphatase activity toward long-chain polyPs (by 90%), whereas that toward polyP3 and polyP4 was much less affected; furthermore, the phosphohydrolase activity toward pppGpp, ATP, and GTP was also decreased (by 30-75%). In contrast, mxPpx1-2C had increased hydrolytic activity compared to mxPpx1. Furthermore, mxPpx2∆C lost the requirement for K+ characteristic for the wild-type enzyme, whereas mxPpx1-2C acquired it. These results suggest that the C-terminal domain of mxPpx2 is necessary for its maximum hydrolytic activity, especially toward long-chain polyPs, and defines mxPpx2 dependency on K+ for activation.
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Affiliation(s)
- Daiki Harita
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan
| | - Kousei Kanie
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan
| | - Yoshio Kimura
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan.
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16
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Colizzi ES, Vroomans RM, Merks RM. Evolution of multicellularity by collective integration of spatial information. eLife 2020; 9:56349. [PMID: 33064078 PMCID: PMC7652420 DOI: 10.7554/elife.56349] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 10/13/2020] [Indexed: 12/28/2022] Open
Abstract
At the origin of multicellularity, cells may have evolved aggregation in response to predation, for functional specialisation or to allow large-scale integration of environmental cues. These group-level properties emerged from the interactions between cells in a group, and determined the selection pressures experienced by these cells. We investigate the evolution of multicellularity with an evolutionary model where cells search for resources by chemotaxis in a shallow, noisy gradient. Cells can evolve their adhesion to others in a periodically changing environment, where a cell's fitness solely depends on its distance from the gradient source. We show that multicellular aggregates evolve because they perform chemotaxis more efficiently than single cells. Only when the environment changes too frequently, a unicellular state evolves which relies on cell dispersal. Both strategies prevent the invasion of the other through interference competition, creating evolutionary bi-stability. Therefore, collective behaviour can be an emergent selective driver for undifferentiated multicellularity.
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Affiliation(s)
| | - Renske Ma Vroomans
- Informatics Institute, University of Amsterdam; Origins Center, Amsterdam, Netherlands
| | - Roeland Mh Merks
- Mathematical Institute, Leiden University; Institute of Biology, Leiden University; Origins Center, Leiden, Netherlands
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17
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Li Y, Jian X, Li Y, Zeng X, Xu L, Khan MU, Lin W. OsPAL2-1 Mediates Allelopathic Interactions Between Rice and Specific Microorganisms in the Rhizosphere Ecosystem. Front Microbiol 2020; 11:1411. [PMID: 32793125 PMCID: PMC7391800 DOI: 10.3389/fmicb.2020.01411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 05/29/2020] [Indexed: 11/13/2022] Open
Abstract
The use of plant allelopathy to control weeds in the field has been generally recognized as a win-win strategy because it is an environmentally friendly and resource-saving method. The mechanism of this natural weed-control method relies on allelochemicals, the rhizosphere microbiome, and their bio-interaction, and exploring the link between allelochemicals and specific microbes helps accelerate the application of allelopathic characteristics in farming. In this study, we used allelopathic rice PI312777 (PI), its genetically modified OsPAL2-1 repression (PR) or overexpression (PO) lines, and non-allelopathic rice Lemont (Le) as donor plants to reveal the bio-interaction between rice allelochemicals and rhizosphere specific microorganisms. The results showed a higher content of phenolic acid exudation from the roots of PI than those of Le, which resulted in a significantly increased population of Myxococcus in the rhizosphere soil. Transgenic PO lines exhibited increasing exudation of phenolic acid, which led to the population of Myxococcus xanthus in the rhizosphere soil of PO to be significantly increased, while PR showed the opposite result in comparison with wild type PI. Exogenous application of phenolic acid induced the growth of M. xanthus, and the expressions of chemotaxis-related genes were up-regulated in M. xanthus. In addition, quercetin was identified in the culture medium; according to the bioassay determination, a quercetin concentration of 0.53 mM inhibited the root length by 60.59%. Our study indicates that OsPAL2-1 is among the efficient genes that regulate rice allelopathy by controlling the synthesis of phenolic acid allelochemicals, and phenolic acid (ferulic acid, FA) induces the chemotactic aggregation of M. xanthus, which promoted the proliferation and aggregation of this microbe. The potential allelochemical, quercetin was generated from the FA-induced M. xanthus cultured medium.
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Affiliation(s)
- Yingzhe Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Xin Jian
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Yue Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Xiaomei Zeng
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Lining Xu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Muhammad Umar Khan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China.,Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
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18
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Zhang Y, Han L, Zhang L, Xu C, Shi X, Hikichi Y, Ohnishi K. Expression of Ralstonia solanacearum type III secretion system is dependent on a novel type 4 pili (T4P) assembly protein (TapV) but is T4P independent. MOLECULAR PLANT PATHOLOGY 2020; 21:777-793. [PMID: 32196936 PMCID: PMC7214476 DOI: 10.1111/mpp.12930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/08/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
Type IV pili (T4P) are virulence factors in various pathogenic bacteria of animals and plants that play important roles in twitching motility, swimming motility, biofilm formation, and adhesion to host cells. Here, we genetically characterized functional roles of a putative T4P assembly protein TapV (Rsc1986 in reference strain GMI1000) and its homologue Rsp0189, which shares 58% amino acid identity with TapV, in Ralstonia solanacearum. Deletion of tapV, but not rsp0189, resulted in significantly impaired twitching motility, swimming motility, and adhesion to tomato roots, which are consistent as phenotypes of the pilA mutant (a known R. solanacearum T4P-deficient mutant). However, unlike the pilA mutant, the tapV mutant produced more biofilm than the wild-type strain. Our gene expression studies revealed that TapV, but not Rsp0189, is important for expression of a type III secretion system (T3SS, a pathogenicity determinant of R. solanacearum) both in vitro and in planta, but it is T4P independent. We further revealed that TapV affected the T3SS expression via the PhcA-TapV-PrhG-HrpB pathway, consistent with previous reports that PhcA positively regulates expression of pilA and prhG. Moreover, deletion of tapV, but not rsp0189, significantly impaired the ability to migrate into and colonize xylem vessels of host plants, but there was no alteration in intercellular proliferation of R. solanacearum in tobacco leaves, which is similar to the pilA mutant. The tapV mutant showed significantly impaired virulence in host plants. This is the first report on the impact of T4P components on the T3SS, providing novel insights into our understanding of various biological functions of T4P and the complex regulatory pathway of T3SS in R. solanacearum.
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Affiliation(s)
- Yong Zhang
- College of Resources and EnvironmentSouthwest UniversityChongqingChina
- Key Laboratory of Efficient Utilization of Soil and Fertilizer ResourcesChongqingChina
| | - Liangliang Han
- College of Resources and EnvironmentSouthwest UniversityChongqingChina
- Research Institute of Molecular GeneticsKochi UniversityKochiJapan
| | - Lichun Zhang
- College of Resources and EnvironmentSouthwest UniversityChongqingChina
- Research Institute of Molecular GeneticsKochi UniversityKochiJapan
| | - Changzheng Xu
- College of Life scienceSouthwest UniversityChongqingChina
| | - Xiaojun Shi
- College of Resources and EnvironmentSouthwest UniversityChongqingChina
- Key Laboratory of Efficient Utilization of Soil and Fertilizer ResourcesChongqingChina
| | - Yasufumi Hikichi
- Laboratory of Plant Pathology and BiotechnologyKochi UniversityKochiJapan
| | - Kouhei Ohnishi
- Research Institute of Molecular GeneticsKochi UniversityKochiJapan
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19
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Maitra A, Srivastava P, Marchetti MC, Ramaswamy S, Lenz M. Swimmer Suspensions on Substrates: Anomalous Stability and Long-Range Order. PHYSICAL REVIEW LETTERS 2020; 124:028002. [PMID: 32004049 DOI: 10.1103/physrevlett.124.028002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 09/08/2019] [Indexed: 06/10/2023]
Abstract
We present a comprehensive theory of the dynamics and fluctuations of a two-dimensional suspension of polar active particles in an incompressible fluid confined to a substrate. We show that, depending on the sign of a single parameter, a state with polar orientational order is anomalously stable (or anomalously unstable), with a nonzero relaxation (or growth) rate for angular fluctuations, not parallel to the ordering direction, at zero wave number. This screening of the broken-symmetry mode in the stable state does lead to conventional rather than giant number fluctuations as argued by Bricard et al., Nature 503, 95 (2013), but their bend instability in a splay-stable flock does not exist and the polar phase has long-range order in two dimensions. Our theory also describes confined three-dimensional thin-film suspensions of active polar particles as well as dense compressible active polar rods, and predicts a flocking transition without a banding instability.
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Affiliation(s)
- Ananyo Maitra
- Sorbonne Université and CNRS, Laboratoire Jean Perrin, F-75005, Paris, France
- LPTMS, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Pragya Srivastava
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, 44 Lincoln's Inn Fields WC2A 3LY, London
- School of Engineering & Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - M Cristina Marchetti
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Sriram Ramaswamy
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560 012, India
- Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, Hyderabad 500 107, India
| | - Martin Lenz
- LPTMS, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
- PMMH, CNRS, ESPCI Paris, PSL University, Sorbonne Université, Université de Paris, F-75005, Paris, France
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20
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Painter KJ. Mathematical models for chemotaxis and their applications in self-organisation phenomena. J Theor Biol 2019; 481:162-182. [DOI: 10.1016/j.jtbi.2018.06.019] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/20/2018] [Accepted: 06/22/2018] [Indexed: 01/31/2023]
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21
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Whitfield DL, Sharma G, Smaldone GT, Singer M. Peripheral rods: a specialized developmental cell type in Myxococcus xanthus. Genomics 2019; 112:1588-1597. [PMID: 31605730 DOI: 10.1016/j.ygeno.2019.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/13/2019] [Accepted: 09/11/2019] [Indexed: 01/08/2023]
Abstract
In response to nutrient deprivation, the ubiquitous Gram-negative soil bacterium Myxococcus xanthus undergoes a well-characterized developmental response, resulting in the formation of a multicellular fruiting body. The center of the fruiting body consists of myxospores; surrounding this structure are rod-shaped peripheral cells. Unlike spores, the peripheral rods are a metabolically active cell type that inhabits nutrient-deprived environments. The survival characteristics exhibited by peripheral rods, protection from oxidative stress and heat shock, are common survival characteristics exhibited by cells in stationary phase including modifications to morphology and metabolism. Vegetative M. xanthus cells undergo a number of physiological changes during the transition into stationary phase similar to other proteobacteria. In M. xanthus, stationary-phase cells are not considered a component of the developmental response and occur when cells are grown on nutrient-rich plates or in dispersed aqueous media. However, this cell type is not routinely studied and little of its physiology is known. Similarities between these two stress-induced cell types led to the question of whether peripheral rods are actually a distinct developmental cell type or simply cells in stationary phase. In this study, we examine the transcriptome of peripheral rods and its relationship to development. This work demonstrates that peripheral rods are in fact a distinct developmentally differentiated cell type. Although peripheral rods and stationary phase cells display similar characteristics, each transcriptomic pattern is unique and quite different from that of any other M. xanthus cell type.
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Affiliation(s)
- Damion L Whitfield
- Dept. of Microbiology and Molecular Genetics, University of California, Davis, CA, USA.
| | - Gaurav Sharma
- Dept. of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Gregory T Smaldone
- Dept. of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Mitchell Singer
- Dept. of Microbiology and Molecular Genetics, University of California, Davis, CA, USA.
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22
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van der Linden MN, Alexander LC, Aarts DGAL, Dauchot O. Interrupted Motility Induced Phase Separation in Aligning Active Colloids. PHYSICAL REVIEW LETTERS 2019; 123:098001. [PMID: 31524482 DOI: 10.1103/physrevlett.123.098001] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/19/2019] [Indexed: 06/10/2023]
Abstract
Switching on high activity in a relatively dense system of active Janus colloids, we observe fast clustering, followed by cluster aggregation towards full phase separation. The phase separation process is however interrupted when large enough clusters start breaking apart. Following the cluster size distribution as a function of time, we identify three successive dynamical regimes. Tracking both the particle positions and orientations, we characterize the structural ordering and alignment in the growing clusters and thereby unveil the mechanisms at play in these regimes. In particular, we identify how alignment between the neighboring particles is responsible for the interruption of the full phase separation. Our large scale quantification of the phase separation kinetics in active colloids points towards the new physics observed when both alignment and short-range repulsions are present.
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Affiliation(s)
- Marjolein N van der Linden
- Gulliver UMR CNRS 7083, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry-University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Lachlan C Alexander
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry-University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Dirk G A L Aarts
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry-University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Olivier Dauchot
- Gulliver UMR CNRS 7083, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
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23
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Guzmán M, Soto R. Nonideal rheology of semidilute bacterial suspensions. Phys Rev E 2019; 99:012613. [PMID: 30780215 DOI: 10.1103/physreve.99.012613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Indexed: 11/07/2022]
Abstract
The rheology of semidilute bacterial suspensions is studied with the tools of kinetic theory, considering binary interactions, going beyond the ideal gas approximation. Two models for the interactions are considered, which encompass both the steric and short-range interactions. In these, swimmers can either align polarly regardless of the state previous to the collision, or they can align axially, ending up antiparallel if the relative angle between directors is large. In both cases, it is found that an ordered phase develops when increasing the density, where the shear stress oscillates with large amplitudes, when a constant shear rate is imposed. This oscillation disappears for large shear rates in a continuous or discontinuous transition, depending on if the aligning is polar or axial, respectively. For pusher swimmers these nonlinear effects can produce an increase on the shear stress, contrary to the prediction of a viscosity reduction made for the dilute regime with the ideal gas approximation.
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Affiliation(s)
- Marcelo Guzmán
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Avenida Blanco Encalada 2008, Santiago, Chile
| | - Rodrigo Soto
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Avenida Blanco Encalada 2008, Santiago, Chile
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24
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Be’er A, Ariel G. A statistical physics view of swarming bacteria. MOVEMENT ECOLOGY 2019; 7:9. [PMID: 30923619 PMCID: PMC6419441 DOI: 10.1186/s40462-019-0153-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/18/2019] [Indexed: 05/18/2023]
Abstract
Bacterial swarming is a collective mode of motion in which cells migrate rapidly over surfaces, forming dynamic patterns of whirls and jets. This review presents a physical point of view of swarming bacteria, with an emphasis on the statistical properties of the swarm dynamics as observed in experiments. The basic physical principles underlying the swarm and their relation to contemporary theories of collective motion and active matter are reviewed and discussed in the context of the biological properties of swarming cells. We suggest a paradigm according to which bacteria have optimized some of their physical properties as a strategy for rapid surface translocation. In other words, cells take advantage of favorable physics, enabling efficient expansion that enhances survival under harsh conditions.
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Affiliation(s)
- Avraham Be’er
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990 Midreshet Ben-Gurion, Israel
- Department of Physics, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
| | - Gil Ariel
- Department of Mathematics, Bar-Ilan University, 52000 Ramat Gan, Israel
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25
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Kappler S, Karmann L, Prudel C, Herrmann J, Caddeu G, Müller R, Vollmar AM, Zahler S, Kazmaier U. Synthesis and Biological Evaluation of Modified Miuraenamides. European J Org Chem 2018. [DOI: 10.1002/ejoc.201801391] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sarah Kappler
- Organic Chemistry; Saarland University; Campus C4.2 66123 Saarbrücken Germany
| | - Lisa Karmann
- Organic Chemistry; Saarland University; Campus C4.2 66123 Saarbrücken Germany
| | - Cynthia Prudel
- Organic Chemistry; Saarland University; Campus C4.2 66123 Saarbrücken Germany
| | - Jennifer Herrmann
- Department Microbial Natural Products; Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS); Saarland University; Campus E8.1 66123 Saarbrücken Germany
| | - Giulia Caddeu
- Department of Pharmacy, Pharmaceutical Biology; Ludwig-Maximilians-University Munich); Butenandtstr. 5-13 81377 München Germany
| | - Rolf Müller
- Department Microbial Natural Products; Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS); Saarland University; Campus E8.1 66123 Saarbrücken Germany
| | - Angelika M. Vollmar
- Department of Pharmacy, Pharmaceutical Biology; Ludwig-Maximilians-University Munich); Butenandtstr. 5-13 81377 München Germany
| | - Stefan Zahler
- Department of Pharmacy, Pharmaceutical Biology; Ludwig-Maximilians-University Munich); Butenandtstr. 5-13 81377 München Germany
| | - Uli Kazmaier
- Organic Chemistry; Saarland University; Campus C4.2 66123 Saarbrücken Germany
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26
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Escaff D, Toral R, Van den Broeck C, Lindenberg K. A continuous-time persistent random walk model for flocking. CHAOS (WOODBURY, N.Y.) 2018; 28:075507. [PMID: 30070507 DOI: 10.1063/1.5027734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A classical random walker is characterized by a random position and velocity. This sort of random walk was originally proposed by Einstein to model Brownian motion and to demonstrate the existence of atoms and molecules. Such a walker represents an inanimate particle driven by environmental fluctuations. On the other hand, there are many examples of so-called "persistent random walkers," including self-propelled particles that are able to move with almost constant speed while randomly changing their direction of motion. Examples include living entities (ranging from flagellated unicellular organisms to complex animals such as birds and fish), as well as synthetic materials. Here we discuss such persistent non-interacting random walkers as a model for active particles. We also present a model that includes interactions among particles, leading to a transition to flocking, that is, to a net flux where the majority of the particles move in the same direction. Moreover, the model exhibits secondary transitions that lead to clustering and more complex spatially structured states of flocking. We analyze all these transitions in terms of bifurcations using a number of mean field strategies (all to all interaction and advection-reaction equations for the spatially structured states), and compare these results with direct numerical simulations of ensembles of these interacting active particles.
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Affiliation(s)
- Daniel Escaff
- Complex Systems Group, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de los Andes, Monseñor Alvaro del Portillo 12455, Las Condes, Santiago, Chile
| | - Raúl Toral
- IFISC (Instituto de Física Interdisciplinar y Sistemas Complejos), Universitat de les Illes Balears-CSIC, Palma de Mallorca 07122, Spain
| | - Christian Van den Broeck
- Hasselt University, B-3500 Hasselt, Belgium and Stellenbosch Institute for Advanced Studies, Matieland 7602, South Africa
| | - Katja Lindenberg
- Department of Chemistry and Biochemistry and BioCircuits Institute, University of California San Diego, La Jolla, California 92093-0340, USA
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27
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Radzvilavicius AL, Blackstone NW. The evolution of individuality revisited. Biol Rev Camb Philos Soc 2018; 93:1620-1633. [DOI: 10.1111/brv.12412] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 02/21/2018] [Accepted: 02/28/2018] [Indexed: 12/28/2022]
Affiliation(s)
| | - Neil W. Blackstone
- Department of Biological Sciences; Northern Illinois University; DeKalb IL 60115 U.S.A
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28
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Taghvafard H, Jardón-Kojakhmetov H, Cao M. Parameter-robustness analysis for a biochemical oscillator model describing the social-behaviour transition phase of myxobacteria. Proc Math Phys Eng Sci 2018; 474:20170499. [PMID: 29434506 DOI: 10.1098/rspa.2017.0499] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/21/2017] [Indexed: 11/12/2022] Open
Abstract
We develop a tool based on bifurcation analysis for parameter-robustness analysis for a class of oscillators and, in particular, examine a biochemical oscillator that describes the transition phase between social behaviours of myxobacteria. Myxobacteria are a particular group of soil bacteria that have two dogmatically different types of social behaviour: when food is abundant they live fairly isolated forming swarms, but when food is scarce, they aggregate into a multicellular organism. In the transition between the two types of behaviours, spatial wave patterns are produced, which is generally believed to be regulated by a certain biochemical clock that controls the direction of myxobacteria's motion. We provide a detailed analysis of such a clock and show that, for the proposed model, there exists some interval in parameter space where the behaviour is robust, i.e. the system behaves similarly for all parameter values. In more mathematical terms, we show the existence and convergence of trajectories to a limit cycle, and provide estimates of the parameter under which such a behaviour occurs. In addition, we show that the reported convergence result is robust, in the sense that any small change in the parameters leads to the same qualitative behaviour of the solution.
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Affiliation(s)
- Hadi Taghvafard
- Engineering and Technology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Hildeberto Jardón-Kojakhmetov
- Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Ming Cao
- Engineering and Technology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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29
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Prathyusha KR, Henkes S, Sknepnek R. Dynamically generated patterns in dense suspensions of active filaments. Phys Rev E 2018; 97:022606. [PMID: 29548173 DOI: 10.1103/physreve.97.022606] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Indexed: 06/08/2023]
Abstract
We use Langevin dynamics simulations to study dynamical behavior of a dense planar layer of active semiflexible filaments. Using the strength of active force and the thermal persistence length as parameters, we map a detailed phase diagram and identify several nonequilibrium phases in this system. In addition to a slowly flowing melt phase, we observe that, for sufficiently high activity, collective flow accompanied by signatures of local polar and nematic order appears in the system. This state is also characterized by strong density fluctuations. Furthermore, we identify an activity-driven crossover from this state of coherently flowing bundles of filaments to a phase with no global flow, formed by individual filaments coiled into rotating spirals. This suggests a mechanism where the system responds to activity by changing the shape of active agents, an effect with no analog in systems of active particles without internal degrees of freedom.
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Affiliation(s)
- K R Prathyusha
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Silke Henkes
- Institute of Complex Systems and Mathematical Biology, Department of Physics, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Rastko Sknepnek
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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30
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Troselj V, Cao P, Wall D. Cell-cell recognition and social networking in bacteria. Environ Microbiol 2017; 20:923-933. [PMID: 29194914 DOI: 10.1111/1462-2920.14005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 01/13/2023]
Abstract
The ability to recognize self and to recognize partnering cells allows microorganisms to build social networks that perform functions beyond the capabilities of the individual. In bacteria, recognition typically involves genetic determinants that provide cell surface receptors or diffusible signalling chemicals to identify proximal cells at the molecular level that can participate in cooperative processes. Social networks also rely on discriminating mechanisms to exclude competing cells from joining and exploiting their groups. In addition to their appropriate genotypes, cell-cell recognition also requires compatible phenotypes, which vary according to environmental cues or exposures as well as stochastic processes that lead to heterogeneity and potential disharmony in the population. Understanding how bacteria identify their social partners and how they synchronize their behaviours to conduct multicellular functions is an expanding field of research. Here, we review recent progress in the field and contrast the various strategies used in recognition and behavioural networking.
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Affiliation(s)
- Vera Troselj
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
| | - Pengbo Cao
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
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31
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Arias Del Angel JA, Escalante AE, Martínez-Castilla LP, Benítez M. An Evo-Devo Perspective on Multicellular Development of Myxobacteria. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:165-178. [PMID: 28217903 DOI: 10.1002/jez.b.22727] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 12/12/2016] [Accepted: 12/25/2016] [Indexed: 11/07/2022]
Abstract
The transition to multicellularity, recognized as one the major transitions in evolution, has occurred independently several times. While multicellular development has been extensively studied in zygotic organisms including plant and animal groups, just a few aggregative multicellular organisms have been employed as model organisms for the study of multicellularity. Studying different evolutionary origins and modes of multicellularity enables comparative analyses that can help identifying lineage-specific aspects of multicellular evolution and generic factors and mechanisms involved in the transition to multicellularity. Among aggregative multicellular organisms, myxobacteria are a valuable system to explore the particularities that aggregation confers to the evolution of multicellularity and mechanisms shared with clonal organisms. Moreover, myxobacteria species develop fruiting bodies displaying a range of morphological diversity. In this review, we aim to synthesize diverse lines of evidence regarding myxobacteria development and discuss them in the context of Evo-Devo concepts and approaches. First, we briefly describe the developmental processes in myxobacteria, present an updated comparative analysis of the genes involved in their developmental processes and discuss these and other lines of evidence in terms of co-option and developmental system drift, two concepts key to Evo-Devo studies. Next, as has been suggested from Evo-Devo approaches, we discuss how broad comparative studies and integration of diverse genetic, physicochemical, and environmental factors into experimental and theoretical models can further our understanding of myxobacterial development, phenotypic variation, and evolution.
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Affiliation(s)
- Juan A Arias Del Angel
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecologiía, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana E Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecologiía, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - León Patricio Martínez-Castilla
- Departamento de Bioquímica, Facultad de Quiímica, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de Ecologiía, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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32
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Pentz JT, Taylor BP, Ratcliff WC. Apoptosis in snowflake yeast: novel trait, or side effect of toxic waste? J R Soc Interface 2017; 13:rsif.2016.0121. [PMID: 27146690 DOI: 10.1098/rsif.2016.0121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/11/2016] [Indexed: 11/12/2022] Open
Abstract
Recent experiments evolving de novo multicellularity in yeast have found that large cluster-forming genotypes also exhibit higher rates of programmed cell death (apoptosis). This was previously interpreted as the evolution of a simple form of cellular division of labour: apoptosis results in the scission of cell-cell connections, allowing snowflake yeast to produce proportionally smaller, faster-growing propagules. Through spatial simulations, Duran-Nebreda and Solé (J. R. Soc. Interface 12, 20140982 (doi:10.1073/pnas.1115323109)) develop the novel null hypothesis that apoptosis is not an adaptation, per se, but is instead caused by the accumulation of toxic metabolites in large clusters. Here we test this hypothesis by synthetically creating unicellular derivatives of snowflake yeast through functional complementation with the ancestral ACE2 allele. We find that multicellular snowflake yeast with elevated apoptosis exhibit a similar rate of apoptosis when cultured as single cells. We also show that larger snowflake yeast clusters tend to contain a greater fraction of older, senescent cells, which may explain why larger clusters of a given genotype are more apoptotic. Our results show that apoptosis is not caused by side effects of spatial structure, such as starvation or waste product accumulation, and are consistent with the hypothesis that elevated apoptosis is a trait that co-evolves with large cluster size.
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Affiliation(s)
- Jennifer T Pentz
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Bradford P Taylor
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - William C Ratcliff
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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33
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Kuzikov AV, Masamrekh RA, Khatri Y, Zavialova MG, Bernhardt R, Archakov AI, Shumyantseva VV. Scrutiny of electrochemically-driven electrocatalysis of C-19 steroid 1α-hydroxylase (CYP260A1) from Sorangium cellulosum So ce56. Anal Biochem 2016; 513:28-35. [PMID: 27567992 DOI: 10.1016/j.ab.2016.08.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/17/2016] [Accepted: 08/19/2016] [Indexed: 01/08/2023]
Abstract
Direct electrochemistry and bioelectrocatalysis of a newly discovered C-19 steroid 1α-hydroxylase (CYP260A1) from the myxobacterium Sorangium cellulosum So ce56 were investigated. CYP260A1 was immobilized on screen-printed graphite electrodes (SPE) modified with gold nanoparticles, stabilized by didodecyldimethylammonium bromide (SPE/DDAB/Au). Cyclic voltammograms in argon-saturated substrate free 0.1 M potassium phosphate buffer, pH 7.4, and in enzyme-substrate complex with androstenedione demonstrated a redox processes with a single redox couple of E(0') of -299 ± 16 mV and -297.5 ± 21 mV (vs. Ag/AgCl), respectively. CYP260A1 exhibited an electrocatalytic activity detected by an increase of the reduction current in the presence of dissolved oxygen and upon addition of the substrate (androstenedione) in the air-saturated buffer. The catalytic current of the enzyme correlated with substrate concentration in the electrochemical system and this dependence can be described by electrochemical Michaelis-Menten model. The products of CYP260A1-depended electrolysis at controlled working electrode potential of androstenedione were analyzed by mass-spectrometry. MS analysis revealed a mono-hydroxylated product of CYP260A1-dependent electrocatalytic reaction towards androstenedione.
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Affiliation(s)
- Alexey V Kuzikov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Moscow 119121, Russia; Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, Moscow 117997, Russia
| | - Rami A Masamrekh
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Moscow 119121, Russia; Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, Moscow 117997, Russia
| | - Yogan Khatri
- Institute of Biochemistry, Saarland University, Saarbruecken 66123, Germany
| | - Maria G Zavialova
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Rita Bernhardt
- Institute of Biochemistry, Saarland University, Saarbruecken 66123, Germany
| | - Alexander I Archakov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Moscow 119121, Russia; Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, Moscow 117997, Russia
| | - Victoria V Shumyantseva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Moscow 119121, Russia; Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, Moscow 117997, Russia.
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34
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Muñoz-Dorado J, Marcos-Torres FJ, García-Bravo E, Moraleda-Muñoz A, Pérez J. Myxobacteria: Moving, Killing, Feeding, and Surviving Together. Front Microbiol 2016; 7:781. [PMID: 27303375 PMCID: PMC4880591 DOI: 10.3389/fmicb.2016.00781] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/09/2016] [Indexed: 11/13/2022] Open
Abstract
Myxococcus xanthus, like other myxobacteria, is a social bacterium that moves and feeds cooperatively in predatory groups. On surfaces, rod-shaped vegetative cells move in search of the prey in a coordinated manner, forming dynamic multicellular groups referred to as swarms. Within the swarms, cells interact with one another and use two separate locomotion systems. Adventurous motility, which drives the movement of individual cells, is associated with the secretion of slime that forms trails at the leading edge of the swarms. It has been proposed that cellular traffic along these trails contributes to M. xanthus social behavior via stigmergic regulation. However, most of the cells travel in groups by using social motility, which is cell contact-dependent and requires a large number of individuals. Exopolysaccharides and the retraction of type IV pili at alternate poles of the cells are the engines associated with social motility. When the swarms encounter prey, the population of M. xanthus lyses and takes up nutrients from nearby cells. This cooperative and highly density-dependent feeding behavior has the advantage that the pool of hydrolytic enzymes and other secondary metabolites secreted by the entire group is shared by the community to optimize the use of the degradation products. This multicellular behavior is especially observed in the absence of nutrients. In this condition, M. xanthus swarms have the ability to organize the gliding movements of 1000s of rods, synchronizing rippling waves of oscillating cells, to form macroscopic fruiting bodies, with three subpopulations of cells showing division of labor. A small fraction of cells either develop into resistant myxospores or remain as peripheral rods, while the majority of cells die, probably to provide nutrients to allow aggregation and spore differentiation. Sporulation within multicellular fruiting bodies has the benefit of enabling survival in hostile environments, and increases germination and growth rates when cells encounter favorable conditions. Herein, we review how these social bacteria cooperate and review the main cell–cell signaling systems used for communication to maintain multicellularity.
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Affiliation(s)
- José Muñoz-Dorado
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada Granada, Spain
| | | | - Elena García-Bravo
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada Granada, Spain
| | - Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada Granada, Spain
| | - Juana Pérez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada Granada, Spain
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Abstract
Bacteria form surface-attached communities, known as biofilms, which are central to bacterial biology and how they affect us. Although surface-attached bacteria often experience strong chemical gradients, it remains unclear whether single cells can effectively perform chemotaxis on surfaces. Here we use microfluidic chemical gradients and massively parallel automated tracking to study the behavior of the pathogen Pseudomonas aeruginosa during early biofilm development. We show that individual cells can efficiently move toward chemoattractants using pili-based "twitching" motility and the Chp chemosensory system. Moreover, we discovered the behavioral mechanism underlying this surface chemotaxis: Cells reverse direction more frequently when moving away from chemoattractant sources. These corrective maneuvers are triggered rapidly, typically before a wayward cell has ventured a fraction of a micron. Our work shows that single bacteria can direct their motion with submicron precision and reveals the hidden potential for chemotaxis within bacterial biofilms.
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Abstract
Outer membrane vesicles (OMVs) are produced from the outer membrane (OM) of myxobacterial cells and are found in large quantities within myxobacterial biofilms. It has been proposed that OMVs are involved in several of the social behaviors exhibited by the myxobacteria, including motility and predation. Proteomic data suggest that specific proteins are either selectively incorporated into or excluded from myxobacterial OMVs, as observed for OMVs of other organisms. Hydrolases are found in large numbers in OMVs, which then transport them to target bacteria. Fusion of OMVs with the OM of Gram-negative cells, or lysis of OMVs next to Gram-positive bacteria, is thought to deliver hydrolases to target cells, causing their lysis. The model myxobacterium Myxococcus xanthus is a predator of other bacteria, and OMVs are likely employed as predatory agents by this organism. The transfer of motility proteins between cells of M. xanthus has been documented, and OMV-mediated transfer provides a convenient mechanism to explain this phenomenon. This review describes the general principles of OMV biology, provides an overview of myxobacterial behavior, summarizes what is currently known about myxobacterial OMVs, and discusses the potential involvement of OMVs in many features of the myxobacterial life-cycle.
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Affiliation(s)
- David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom.
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37
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Shumyantseva V, Kuzikov A, Masamrekh R, Khatri Y, Zavialova M, Bernhardt R, Archakov A. Direct electrochemistry of CYP109C1, CYP109C2 and CYP109D1 from Sorangium cellulosum So ce56. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.01.162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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38
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Keane R, Berleman J. The predatory life cycle of Myxococcus xanthus. Microbiology (Reading) 2016; 162:1-11. [DOI: 10.1099/mic.0.000208] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ryan Keane
- Department of Biology, Saint Mary's College, Moraga, CA 94556, USA
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James Berleman
- Department of Biology, Saint Mary's College, Moraga, CA 94556, USA
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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39
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Imhof S, Roditi I. The Social Life of African Trypanosomes. Trends Parasitol 2015; 31:490-498. [PMID: 26433252 DOI: 10.1016/j.pt.2015.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/28/2015] [Accepted: 06/24/2015] [Indexed: 01/03/2023]
Abstract
The unicellular parasite Trypanosoma brucei shuttles between its definitive host, the tsetse fly, and various mammals including humans. In the fly digestive tract, T. brucei must first migrate to the ectoperitrophic space, establish a persistent infection of the midgut and then migrate to the salivary glands before being transmitted to a new mammalian host. In 2010, it was shown that insect stages of the parasite (procyclic forms) exhibit social motility (SoMo) when cultured on a semi-solid surface, and it was postulated that this behaviour might reflect a migration step in the tsetse fly. Now, almost 5 years after the initial report, several new publications shed some light on the biological function of SoMo and provide insights into the underlying signalling pathways.
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Affiliation(s)
- Simon Imhof
- Institute of Cell Biology, University of Bern, Bern, Switzerland; Graduate School for Biomedical and Cellular Science, University of Bern, Bern, Switzerland
| | - Isabel Roditi
- Institute of Cell Biology, University of Bern, Bern, Switzerland.
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40
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41
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Saada EA, DeMarco SF, Shimogawa MM, Hill KL. "With a Little Help from My Friends"-Social Motility in Trypanosoma brucei. PLoS Pathog 2015; 11:e1005272. [PMID: 26679190 PMCID: PMC4683075 DOI: 10.1371/journal.ppat.1005272] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Edwin A. Saada
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Stephanie F. DeMarco
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Michelle M. Shimogawa
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Kent L. Hill
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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Seccareccia I, Kost C, Nett M. Quantitative Analysis of Lysobacter Predation. Appl Environ Microbiol 2015; 81:7098-105. [PMID: 26231654 PMCID: PMC4579460 DOI: 10.1128/aem.01781-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/28/2015] [Indexed: 02/01/2023] Open
Abstract
Bacteria of the genus Lysobacter are considered to be facultative predators that use a feeding strategy similar to that of myxobacteria. Experimental data supporting this assumption, however, are scarce. Therefore, the predatory activities of three Lysobacter species were tested in the prey spot plate assay and in the lawn predation assay, which are commonly used to analyze myxobacterial predation. Surprisingly, only one of the tested Lysobacter species showed predatory behavior in the two assays. This result suggested that not all Lysobacter strains are predatory or, alternatively, that the assays were not appropriate for determining the predatory potential of this bacterial group. To differentiate between the two scenarios, predation was tested in a CFU-based bioassay. For this purpose, defined numbers of Lysobacter cells were mixed together with potential prey bacteria featuring phenotypic markers, such as distinctive pigmentation or antibiotic resistance. After 24 h, cocultivated cells were streaked out on agar plates and sizes of bacterial populations were individually determined by counting the respective colonies. Using the CFU-based predation assay, we observed that Lysobacter spp. strongly antagonized other bacteria under nutrient-deficient conditions. Simultaneously, the Lysobacter population was increasing, which together with the killing of the cocultured bacteria indicated predation. Variation of the predator/prey ratio revealed that all three Lysobacter species tested needed to outnumber their prey for efficient predation, suggesting that they exclusively practiced group predation. In summary, the CFU-based predation assay not only enabled the quantification of prey killing and consumption by Lysobacter spp. but also provided insights into their mode of predation.
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Affiliation(s)
- Ivana Seccareccia
- Secondary Metabolism of Predatory Bacteria Junior Research Group, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Markus Nett
- Secondary Metabolism of Predatory Bacteria Junior Research Group, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
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Balagam R, Igoshin OA. Mechanism for Collective Cell Alignment in Myxococcus xanthus Bacteria. PLoS Comput Biol 2015; 11:e1004474. [PMID: 26308508 PMCID: PMC4550276 DOI: 10.1371/journal.pcbi.1004474] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 07/28/2015] [Indexed: 11/19/2022] Open
Abstract
Myxococcus xanthus cells self-organize into aligned groups, clusters, at various stages of their lifecycle. Formation of these clusters is crucial for the complex dynamic multi-cellular behavior of these bacteria. However, the mechanism underlying the cell alignment and clustering is not fully understood. Motivated by studies of clustering in self-propelled rods, we hypothesized that M. xanthus cells can align and form clusters through pure mechanical interactions among cells and between cells and substrate. We test this hypothesis using an agent-based simulation framework in which each agent is based on the biophysical model of an individual M. xanthus cell. We show that model agents, under realistic cell flexibility values, can align and form cell clusters but only when periodic reversals of cell directions are suppressed. However, by extending our model to introduce the observed ability of cells to deposit and follow slime trails, we show that effective trail-following leads to clusters in reversing cells. Furthermore, we conclude that mechanical cell alignment combined with slime-trail-following is sufficient to explain the distinct clustering behaviors observed for wild-type and non-reversing M. xanthus mutants in recent experiments. Our results are robust to variation in model parameters, match the experimentally observed trends and can be applied to understand surface motility patterns of other bacterial species.
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Affiliation(s)
- Rajesh Balagam
- Department of Bioengineering and Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - Oleg A. Igoshin
- Department of Bioengineering and Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- * E-mail:
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How Myxobacteria Cooperate. J Mol Biol 2015; 427:3709-21. [PMID: 26254571 DOI: 10.1016/j.jmb.2015.07.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 11/22/2022]
Abstract
Prokaryotes often reside in groups where a high degree of relatedness has allowed the evolution of cooperative behaviors. However, very few bacteria or archaea have made the successful transition from unicellular to obligate multicellular life. A notable exception is the myxobacteria, in which cells cooperate to perform group functions highlighted by fruiting body development, an obligate multicellular function. Like all multicellular organisms, myxobacteria face challenges in how to organize and maintain multicellularity. These challenges include maintaining population homeostasis, carrying out tissue repair and regulating the behavior of non-cooperators. Here, we describe the major cooperative behaviors that myxobacteria use: motility, predation and development. In addition, this review emphasizes recent discoveries in the social behavior of outer membrane exchange, wherein kin share outer membrane contents. Finally, we review evidence that outer membrane exchange may be involved in regulating population homeostasis, thus serving as a social tool for myxobacteria to make the cyclic transitions from unicellular to multicellular states.
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Abstract
The gastric pathogen Helicobacter pylori forms biofilms on abiotic and biotic surfaces. We have shown previously that H. pylori perceives the quorum signal autoinducer-2 (AI-2) as a chemorepellent. We report here that H. pylori chemorepulsion from endogenous AI-2 influences the proportions and spatial organization of cells within biofilms. Strains that fail to produce AI-2 (∆luxS strains) or are defective for chemotaxis (∆cheA strains) formed more spatially homogenous biofilms with a greater proportion of adherent versus planktonic cells than wild-type biofilms. Reciprocally, a strain that overproduced AI-2 (luxSOP) formed biofilms with proportionally fewer adherent cells. Along with the known AI-2 chemoreceptor, TlpB, we identified AibA and AibB, two novel periplasmic binding proteins that are required for the AI-2 chemorepulsion response. Disruptions in any of the proteins required for AI-2 chemotaxis recapitulated the biofilm adherence and spatial organization phenotype of the ∆luxS mutant. Furthermore, exogenous administration of AI-2 was sufficient to decrease the proportion of adherent cells in biofilms and promote dispersal of cells from biofilms in a chemotaxis-dependent manner. Finally, we found that disruption of AI-2 production or AI-2 chemotaxis resulted in increased clustering of cells in microcolonies on cultured epithelial cells. We conclude that chemotaxis from AI-2 is a determinant of H. pylori biofilm spatial organization and dispersal. Bacterial biofilms are ubiquitous in nature, but the mechanisms governing their assembly and spatial organization are not fully understood. Bacterial communication through quorum sensing has been shown to influence biofilm growth through the regulation of biofilm genes. Our study revealed a new role for quorum sensing in biofilms through rapid chemotactic responses to quorum signals. Specifically, we studied how chemorepulsion of Helicobacter pylori from the universal quorum signal autoinducer-2 (AI-2) shapes the spatial organization of its biofilms. We demonstrate that the chemorepulsive response of H. pylori to AI-2 is necessary to promote its dispersal from biofilms grown on both abiotic and biotic surfaces and is sufficient to promote dispersal in a chemotaxis-dependent manner. This work has broad implications for understanding the mechanisms by which endogenously produced microbial compounds shape the assembly and spatial organization of microbial communities in their environments.
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Development of Spatial Distribution Patterns by Biofilm Cells. Appl Environ Microbiol 2015; 81:6120-8. [PMID: 26116674 DOI: 10.1128/aem.01614-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/19/2015] [Indexed: 01/14/2023] Open
Abstract
Confined spatial patterns of microbial distribution are prevalent in nature, such as in microbial mats, soil communities, and water stream biofilms. The symbiotic two-species consortium of Pseudomonas putida and Acinetobacter sp. strain C6, originally isolated from a creosote-polluted aquifer, has evolved a distinct spatial organization in the laboratory that is characterized by an increased fitness and productivity. In this consortium, P. putida is reliant on microcolonies formed by Acinetobacter sp. C6, to which it attaches. Here we describe the processes that lead to the microcolony pattern by Acinetobacter sp. C6. Ecological spatial pattern analyses revealed that the microcolonies were not entirely randomly distributed and instead were arranged in a uniform pattern. Detailed time-lapse confocal microscopy at the single-cell level demonstrated that the spatial pattern was the result of an intriguing self-organization: small multicellular clusters moved along the surface to fuse with one another to form microcolonies. This active distribution capability was dependent on environmental factors (carbon source and oxygen) and historical contingency (formation of phenotypic variants). The findings of this study are discussed in the context of species distribution patterns observed in macroecology, and we summarize observations about the processes involved in coadaptation between P. putida and Acinetobacter sp. C6. Our results contribute to an understanding of spatial species distribution patterns as they are observed in nature, as well as the ecology of engineered communities that have the potential for enhanced and sustainable bioprocessing capacity.
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Andringa TC, Bosch KAVD, Wijermans N. Cognition from life: the two modes of cognition that underlie moral behavior. Front Psychol 2015; 6:362. [PMID: 25954212 PMCID: PMC4404729 DOI: 10.3389/fpsyg.2015.00362] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 03/15/2015] [Indexed: 11/13/2022] Open
Abstract
We argue that the capacity to live life to the benefit of self and others originates in the defining properties of life. These lead to two modes of cognition; the coping mode that is preoccupied with the satisfaction of pressing needs and the co-creation mode that aims at the realization of a world where pressing needs occur less frequently. We have used the Rule of Conservative Changes - stating that new functions can only scaffold on evolutionary older, yet highly stable functions - to predict that the interplay of these two modes define a number of core functions in psychology associated with moral behavior. We explore this prediction with five examples reflecting different theoretical approaches to human cognition and action selection. We conclude the paper with the observation that science is currently dominated by the coping mode and that the benefits of the co-creation mode may be necessary to generate realistic prospects for a modern synthesis in the sciences of the mind.
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Affiliation(s)
- Tjeerd C Andringa
- Artificial Intelligence and Cognitive Engineering, University of Groningen Groningen, Netherlands
| | | | - Nanda Wijermans
- Stockholm Resilience Centre, Stockholm University Stockholm, Sweden
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Elgeti J, Winkler RG, Gompper G. Physics of microswimmers--single particle motion and collective behavior: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:056601. [PMID: 25919479 DOI: 10.1088/0034-4885/78/5/056601] [Citation(s) in RCA: 647] [Impact Index Per Article: 71.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Locomotion and transport of microorganisms in fluids is an essential aspect of life. Search for food, orientation toward light, spreading of off-spring, and the formation of colonies are only possible due to locomotion. Swimming at the microscale occurs at low Reynolds numbers, where fluid friction and viscosity dominates over inertia. Here, evolution achieved propulsion mechanisms, which overcome and even exploit drag. Prominent propulsion mechanisms are rotating helical flagella, exploited by many bacteria, and snake-like or whip-like motion of eukaryotic flagella, utilized by sperm and algae. For artificial microswimmers, alternative concepts to convert chemical energy or heat into directed motion can be employed, which are potentially more efficient. The dynamics of microswimmers comprises many facets, which are all required to achieve locomotion. In this article, we review the physics of locomotion of biological and synthetic microswimmers, and the collective behavior of their assemblies. Starting from individual microswimmers, we describe the various propulsion mechanism of biological and synthetic systems and address the hydrodynamic aspects of swimming. This comprises synchronization and the concerted beating of flagella and cilia. In addition, the swimming behavior next to surfaces is examined. Finally, collective and cooperate phenomena of various types of isotropic and anisotropic swimmers with and without hydrodynamic interactions are discussed.
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Affiliation(s)
- J Elgeti
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
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Janulevicius A, van Loosdrecht M, Picioreanu C. Short-range guiding can result in the formation of circular aggregates in myxobacteria populations. PLoS Comput Biol 2015; 11:e1004213. [PMID: 25928112 PMCID: PMC4415783 DOI: 10.1371/journal.pcbi.1004213] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 02/25/2015] [Indexed: 12/02/2022] Open
Abstract
Myxobacteria are social bacteria that upon starvation form multicellular fruiting bodies whose shape in different species can range from simple mounds to elaborate tree-like structures. The formation of fruiting bodies is a result of collective cell movement on a solid surface. In the course of development, groups of flexible rod-shaped cells form streams and move in circular or spiral patterns to form aggregation centers that can become sites of fruiting body formation. The mechanisms of such cell movement patterns are not well understood. It has been suggested that myxobacterial development depends on short-range contact-mediated interactions between individual cells, i.e. cell aggregation does not require long-range signaling in the population. In this study, by means of a computational mass-spring model, we investigate what types of short-range interactions between cells can result in the formation of streams and circular aggregates during myxobacterial development. We consider short-range head-to-tail guiding between individual cells, whereby movement direction of the head of one cell is affected by the nearby presence of the tail of another cell. We demonstrate that stable streams and circular aggregates can arise only when the trailing cell, in addition to being steered by the tail of the leading cell, is able to speed up to catch up with it. It is suggested that necessary head-to-tail interactions between cells can arise from physical adhesion, response to a diffusible substance or slime extruded by cells, or pulling by motility engine pili. Finally, we consider a case of long-range guiding between cells and show that circular aggregates are able to form without cells increasing speed. These findings present a possibility to discriminate between short-range and long-range guiding mechanisms in myxobacteria by experimentally measuring distribution of cell speeds in circular aggregates. Myxobacteria are social bacteria that upon starvation form multicellular fruiting bodies whose shape in different species can range from simple mounds to elaborate tree-like structures. The formation of fruiting bodies is a result of collective cell movement on a solid surface. Since collective cell motility during biological morphogenesis is also common in higher organisms, myxobacteria serve as a relatively simple model organism to study multicellular movement, organization and development. In the course of myxobacterial development, groups of flexible rod-shaped cells form streams and move in circular or spiral patterns to form aggregation centers that can become sites of fruiting body formation. The mechanisms of such cell movement patterns are not well understood. In this study, by means of a computational mass-spring model, we demonstrate that the formation of streams and circular aggregates during myxobacterial development can be explained by short-range head-to-tail guiding between individual cells, whereby movement direction of the head of one cell is affected by the nearby presence of the tail of another cell. We suggest that such interactions between cells can result from physical adhesion, response to a diffusible substance or slime extruded by cells, or the action of cell motility engine.
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Affiliation(s)
- Albertas Janulevicius
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
- * E-mail:
| | - Mark van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Cristian Picioreanu
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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50
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Virga EG. Dissipative shocks behind bacteria gliding. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:rsta.2013.0360. [PMID: 25332385 DOI: 10.1098/rsta.2013.0360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Gliding is a means of locomotion on rigid substrates used by a number of bacteria, including myxobacteria and cyanobacteria. One of the hypotheses advanced to explain this motility mechanism hinges on the role played by the slime filaments continuously extruded from gliding bacteria. This paper solves, in full, a non-linear mechanical theory that treats as dissipative shocks both the point where the extruded slime filament comes into contact with the substrate, called the filament's foot, and the pore on the bacterium outer surface from where the filament is ejected. I prove that kinematic compatibility for shock propagation requires that the bacterium uniform gliding velocity (relative to the substrate) and the slime ejecting velocity (relative to the bacterium) must be equal, a coincidence that seems to have already been observed.
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Affiliation(s)
- Epifanio G Virga
- Dipartimento di Matematica, Università di Pavia, Via Ferrata 5, 27100 Pavia, Italy
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