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Schaal KA, Yu YTN, Vasse M, Velicer GJ. Allopatric divergence of cooperators confers cheating resistance and limits effects of a defector mutation. BMC Ecol Evol 2022; 22:141. [PMID: 36510120 PMCID: PMC9746145 DOI: 10.1186/s12862-022-02094-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Social defectors may meet diverse cooperators. Genotype-by-genotype interactions may constrain the ranges of cooperators upon which particular defectors can cheat, limiting cheater spread. Upon starvation, the soil bacterium Myxococcus xanthus cooperatively develops into spore-bearing fruiting bodies, using a complex regulatory network and several intercellular signals. Some strains (cheaters) are unable to sporulate effectively in pure culture due to mutations that reduce signal production but can exploit and outcompete cooperators within mixed groups. RESULTS In this study, interactions between a cheater disrupted at the signaling gene csgA and allopatrically diversified cooperators reveal a very small cheating range. Expectedly, the cheater failed to cheat on all natural-isolate cooperators owing to non-cheater-specific antagonisms. Surprisingly, some lab-evolved cooperators had already exited the csgA mutant's cheating range after accumulating fewer than 20 mutations and without experiencing cheating during evolution. Cooperators might also diversify in the potential for a mutation to reduce expression of a cooperative trait or generate a cheating phenotype. A new csgA mutation constructed in several highly diverged cooperators generated diverse sporulation phenotypes, ranging from a complete defect to no defect, indicating that genetic backgrounds can limit the set of genomes in which a mutation creates a defector. CONCLUSIONS Our results demonstrate that natural populations may feature geographic mosaics of cooperators that have diversified in their susceptibility to particular cheaters, limiting defectors' cheating ranges and preventing them from spreading. This diversification may also lead to variation in the phenotypes generated by any given cooperation-gene mutation, further decreasing the chance of a cheater emerging which threatens the persistence of cooperation in the system.
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Affiliation(s)
- Kaitlin A. Schaal
- grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, 8092 Zurich, Switzerland
| | - Yuen-Tsu Nicco Yu
- grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, 8092 Zurich, Switzerland
| | - Marie Vasse
- grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, 8092 Zurich, Switzerland ,grid.121334.60000 0001 2097 0141Institute MIVEGEC (UMR 5290 CNRS, IRD, UM), 34394 Montpellier, France
| | - Gregory J. Velicer
- grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, 8092 Zurich, Switzerland
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Dye KJ, Yang Z. Analysis of Myxococcus xanthus Vegetative Biofilms With Microtiter Plates. Front Microbiol 2022; 13:894562. [PMID: 35572678 PMCID: PMC9100584 DOI: 10.3389/fmicb.2022.894562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
The bacterium Myxococcus xanthus forms both developmental and vegetative types of biofilms. While the former has been studied on both agar plates and submerged surfaces, the latter has been investigated predominantly on agar surfaces as swarming colonies. Here we describe the development of a microplate-based assay for the submerged biofilms of M. xanthus under vegetative conditions. We examined the impacts of inoculation, aeration, and temperature to optimize the conditions for the assay. Aeration was observed to be critical for the effective development of submerged biofilms by M. xanthus, an obligate aerobic bacterium. In addition, temperature plays an important role in the development of M. xanthus submerged biofilms. It is well established that the formation of submerged biofilms by many bacteria requires both exopolysaccharide (EPS) and the type IV pilus (T4P). EPS constitutes part of the biofilm matrix that maintains and organizes bacterial biofilms while the T4P facilitates surface attachment as adhesins. For validation, we used our biofilm assay to examine a multitude of M. xanthus strains with various EPS and T4P phenotypes. The results indicate that the levels of EPS, but not of piliation, positively correlate with submerged biofilm formation in M. xanthus.
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Wang Y, Li T, Xue W, Zheng Y, Wang Y, Zhang N, Zhao Y, Wang J, Li Y, Wang C, Hu W. Physicochemical and Biological Insights Into the Molecular Interactions Between Extracellular DNA and Exopolysaccharides in Myxococcus xanthus Biofilms. Front Microbiol 2022; 13:861865. [PMID: 35531272 PMCID: PMC9073016 DOI: 10.3389/fmicb.2022.861865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Extracellular DNA (eDNA) is a critical component in the extracellular matrix (ECM) of bacterial biofilms, while little is known about the mechanisms underlying how eDNA integrates into the ECM through potential macromolecular interactions. Myxococcus xanthus biofilm was employed as a suitable model for the investigation due to the co-distribution of eDNA and exopolysaccharides (EPS) owing to their direct interactions in the ECM. DNA is able to combine with M. xanthus EPS to form a macromolecular conjugate, which is dominated by the electrostatic forces participating in the polymer-polymer interactions. Without intercalation binding, DNA-EPS interactions exhibit a certain degree of reversibility. Acting as a strong extracellular framework during biofilm formation process, the eDNA-EPS complex not only facilitates the initial cell adhesion and subsequent establishment of ECM architecture, but also renders cells within biofilms stress resistances that are relevant to the survival of M. xanthus in some hostile environments. Furthermore, the EPS protects the conjugated DNA from the degradation by nucleic acid hydrolases, which leads to the continuous and stable existence of eDNA in the native ECM of M. xanthus biofilms. These results will shed light on developing prevention and treatment strategies against biofilm-related risks.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Tingyi Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Weiwei Xue
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yue Zheng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yipeng Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Ning Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yue Zhao
- College of Pharmaceutical Science, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jing Wang
- College of Pharmaceutical Science, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Chuandong Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
- *Correspondence: Chuandong Wang,
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
- Wei Hu,
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Community Profile and Drivers of Predatory Myxobacteria under Different Compost Manures. Microorganisms 2021; 9:microorganisms9112193. [PMID: 34835319 PMCID: PMC8622275 DOI: 10.3390/microorganisms9112193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
Myxobacteria are unique predatory microorganisms with a distinctive social lifestyle. These taxa play key roles in the microbial food webs in different ecosystems and regulate the community structures of soil microbial communities. Compared with conditions under conventional management, myxobacteria abundance increases in the organic soil, which could be related to the presence of abundant myxobacteria in the applied compost manure during organic conditions. In the present study,16S rRNA genes sequencing technology was used to investigate the community profile and drivers of predatory myxobacteria in four common compost manures. According to the results, there was a significant difference in predatory myxobacteria community structure among different compost manure treatments (p < 0.05). The alpha-diversity indices of myxobacteria community under swine manure compost were the lowest (Observed OTU richness = 13.25, Chao1 = 14.83, Shannon = 0.61), and those under wormcast were the highest (Observed OTU richness = 30.25, Chao1 = 31.65, Shannon = 2.62). Bacterial community diversity and Mg2+ and Ca2+ concentrations were the major factors influencing the myxobacteria community under different compost manure treatments. In addition, organic carbon, pH, and total nitrogen influenced the community profile of myxobacteria in compost manure. The interaction between myxobacteria and specific bacterial taxa (Micrococcales) in compost manure may explain the influence of bacteria on myxobacteria community structure. Further investigations on the in-situ community profile of predatory myxobacteria and the key microorganism influencing their community would advance our understanding of the community profile and functions of predatory microorganisms in the microbial world.
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Myxobacterial Genomics and Post-Genomics: A Review of Genome Biology, Genome Sequences and Related 'Omics Studies. Microorganisms 2021; 9:microorganisms9102143. [PMID: 34683464 PMCID: PMC8538405 DOI: 10.3390/microorganisms9102143] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/27/2022] Open
Abstract
Myxobacteria are fascinating and complex microbes. They prey upon other members of the soil microbiome by secreting antimicrobial proteins and metabolites, and will undergo multicellular development if starved. The genome sequence of the model myxobacterium Myxococcus xanthus DK1622 was published in 2006 and 15 years later, 163 myxobacterial genome sequences have now been made public. This explosion in genomic data has enabled comparative genomics analyses to be performed across the taxon, providing important insights into myxobacterial gene conservation and evolution. The availability of myxobacterial genome sequences has allowed system-wide functional genomic investigations into entire classes of genes. It has also enabled post-genomic technologies to be applied to myxobacteria, including transcriptome analyses (microarrays and RNA-seq), proteome studies (gel-based and gel-free), investigations into protein–DNA interactions (ChIP-seq) and metabolism. Here, we review myxobacterial genome sequencing, and summarise the insights into myxobacterial biology that have emerged as a result. We also outline the application of functional genomics and post-genomic approaches in myxobacterial research, highlighting important findings to emerge from seminal studies. The review also provides a comprehensive guide to the genomic datasets available in mid-2021 for myxobacteria (including 24 genomes that we have sequenced and which are described here for the first time).
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Saïdi F, Jolivet NY, Lemon DJ, Nakamura A, Belgrave AM, Garza AG, Veyrier FJ, Islam ST. Bacterial glycocalyx integrity drives multicellular swarm biofilm dynamism. Mol Microbiol 2021; 116:1151-1172. [PMID: 34455651 DOI: 10.1111/mmi.14803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/24/2022]
Abstract
Exopolysaccharide (EPS) layers on the bacterial cell surface are key determinants of biofilm establishment and maintenance, leading to the formation of higher-order 3D structures that confer numerous survival benefits to a cell community. In addition to a specific cell-associated EPS glycocalyx, we recently revealed that the social δ-proteobacterium Myxococcus xanthus secretes a novel biosurfactant polysaccharide (BPS) to the extracellular milieu. Together, secretion of the two polymers (EPS and BPS) is required for type IV pilus (T4P)-dependent swarm expansion via spatio-specific biofilm expression profiles. Thus the synergy between EPS and BPS secretion somehow modulates the multicellular lifecycle of M. xanthus. Herein, we demonstrate that BPS secretion functionally alters the EPS glycocalyx via destabilization of the latter, fundamentally changing the characteristics of the cell surface. This impacts motility behaviors at the single-cell level and the aggregative capacity of cells in groups via cell-surface EPS fibril formation as well as T4P production, stability, and positioning. These changes modulate the structure of swarm biofilms via cell layering, likely contributing to the formation of internal swarm polysaccharide architecture. Together, these data reveal the manner by which the combined secretion of two distinct polymers induces single-cell changes that modulate swarm biofilm communities.
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Affiliation(s)
- Fares Saïdi
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - Nicolas Y Jolivet
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
| | - David J Lemon
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Arnaldo Nakamura
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
| | - Akeisha M Belgrave
- Integrated Sciences Program, Harrisburg University of Science & Technology, Harrisburg, Pennsylvania, USA
| | - Anthony G Garza
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Frédéric J Veyrier
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada
| | - Salim T Islam
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Institut Pasteur International Network, Laval, Quebec, Canada.,PROTEO, The Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Québec, Quebec, Canada
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7
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Izzat S, Rachid S, Ajdidi A, El-Nakady YA, Liu XX, Ye BC, Müller R. The ROK like protein of Myxococcus xanthus DK1622 acts as a pleiotropic transcriptional regulator for secondary metabolism. J Biotechnol 2020; 311:25-34. [PMID: 32057784 DOI: 10.1016/j.jbiotec.2020.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/03/2020] [Accepted: 02/10/2020] [Indexed: 11/17/2022]
Abstract
Myxococcus xanthus DK1622 is known as a proficient producer of different kinds of secondary metabolites (SM) with various biological activities, including myxovirescin A, myxalamide A, myxochromide A and DKxanthene. Low production of SM in the wild type bacteria makes searching for production optimization methods highly desirable. Identification and induction of endogenous key molecular feature(s) regulating the production level of the metabolites remain promising, while heterologous expression of the biosynthetic genes is not always efficient because of various complicating factors including codon usage bias. This study established proteomic and molecular approaches to elucidate the regulatory roles of the ROK regulatory protein in the modification of secondary metabolite biosynthesis. Interestingly, the results revealed that rok inactivation significantly reduced the production of the SM and also changed the motility in the bacteria. Electrophoretic mobility shift assay using purified ROK protein indicated a direct enhancement of the promoters encoding transcription of the DKxanthene, myxochelin A, and myxalamide A biosynthesis machinery. Comparative proteomic analysis by two-dimensional fluorescence difference in-gel electrophoresis (2D-DIGE) was employed to identify the protein profiles of the wild type and rok mutant strains during early and late logarithmic growth phases of the bacterial culture. Resulting data demonstrated overall 130 differently altered proteins by the effect of the rok gene mutation, including putative proteins suspected to be involved in transcriptional regulation, carbohydrate metabolism, development, spore formation, and motility. Except for a slight induction seen in the production of myxovirescin A in a rok over-expression background, no changes were found in the formation of the other SM. From the outcome of our investigation, it is possible to conclude that ROK acts as a pleiotropic regulator of secondary metabolite formation and development in M. xanthus, while its direct effects still remain speculative. More experiments are required to elucidate in detail the variable regulation effects of the protein and to explore applicable approaches for generating valuable SM in this bacterium.
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Affiliation(s)
- Selar Izzat
- Department of Biology, School of Science and Health, Koya University, Koysinjaq, Kurdistan Region, Iraq
| | - Shwan Rachid
- Charmo Research Center, Charmo University, 46023 Chamchamal-Sulaimani, Iraq; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
| | - Ahmad Ajdidi
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Yasser A El-Nakady
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123 Saarbrücken, Germany; Zoology Department, College of Science, King Saud University, P.O. Box 2455, 11415 Riyadh - Saudi Arabia
| | - Xin-Xin Liu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
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8
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Chen S, Sun S, Korfanty GA, Liu J, Xiang H. A Halocin Promotes DNA Uptake in Haloferax mediterranei. Front Microbiol 2019; 10:1960. [PMID: 31620096 PMCID: PMC6759562 DOI: 10.3389/fmicb.2019.01960] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/09/2019] [Indexed: 11/13/2022] Open
Abstract
Halocins are antimicrobial peptides or proteins that are produced by halophilic archaea. Although their function in inhibiting the growth of closely related haloarchaeal strains is well known, other physiological functions of halocins have also been proposed in recent years. To unveil the possible function and mechanism of halocins in DNA uptake, the halocin H4 producing strain Haloferax mediterranei DF50-ΔEPS (incapable of EPS production) was used in this study. We found that deletion of the halH4 resulted in the strain DF50-ΔEPSΔhalH4 which exhibited loss of natural DNA uptake ability. Moreover, supernatants of the halocin producing strain were capable of inducing the ability to uptake DNA. Obviously, halocin is likely responsible for inducing DNA uptake. Cell surface ultrastructures of these strains are varied from strains DF50-ΔEPS to DF50-ΔEPSΔhalH4. The cell surface of strain DF50-ΔEPS is rough due to numerous pinholes, while that of the strain DF50-ΔEPSΔhalH4 is smooth without visible pinholes. The morphology of the halH4 complemented strain, DF50-ΔEPSΔhalH4::H4, shows an intermediate phenotype between strains DF50-ΔEPS and DF50-ΔEPSΔhalH4. We speculate that halocin H4 may accelerate DNA uptake by perforating the cell surface ultrastructure. The halocin H4 may represent a novel inducer or activator of DNA uptake in Hfx. mediterranei.
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Affiliation(s)
- Shaoxing Chen
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Siqi Sun
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | | | - Jingwen Liu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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9
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Leong CG, Bloomfield RA, Boyd CA, Dornbusch AJ, Lieber L, Liu F, Owen A, Slay E, Lang KM, Lostroh CP. The role of core and accessory type IV pilus genes in natural transformation and twitching motility in the bacterium Acinetobacter baylyi. PLoS One 2017; 12:e0182139. [PMID: 28771515 PMCID: PMC5542475 DOI: 10.1371/journal.pone.0182139] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/12/2017] [Indexed: 11/21/2022] Open
Abstract
Here we present an examination of type IV pilus genes associated with competence and twitching in the bacterium Acinetobacter baylyi (strain ADP1, BD413). We used bioinformatics to identify potential competence and twitching genes and their operons. We measured the competence and twitching phenotypes of the bioinformatically-identified genes. These results demonstrate that competence and twitching in A. baylyi both rely upon a core of the same type IV pilus proteins. The core includes the inner membrane assembly platform (PilC), a periplasmic assemblage connecting the inner membrane assembly platform to the secretin (ComM), a secretin (ComQ) and its associated pilotin (PilF) that assists with secretin assembly and localization, both cytoplasmic pilus retraction ATPases (PilU, PilT), and pilins (ComP, ComB, PilX). Proteins not needed for both competence and twitching are instead found to specialize in either of the two traits. The pilins are varied in their specialization with some required for either competence (FimT) and others for twitching (ComE). The protein that transports DNA across the inner membrane (ComA) specializes in competence, while signal transduction proteins (PilG, PilS, and PilR) specialize in twitching. Taken together our results suggest that the function of accessory proteins should not be based on homology alone. In addition the results suggest that in A. baylyi the mechanisms of natural transformation and twitching are mediated by the same set of core Type IV pilus proteins with distinct specialized proteins required for each phenotype. Finally, since competence requires multiple pilins as well as both pilus retraction motors PilU and PilT, this suggests that A. baylyi employs a pilus in natural transformation.
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Affiliation(s)
- Colleen G. Leong
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Rebecca A. Bloomfield
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Caroline A. Boyd
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Amber J. Dornbusch
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Leah Lieber
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Flora Liu
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Amie Owen
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Erin Slay
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Kristine M. Lang
- Department of Physics, Colorado College, Colorado Springs, Colorado, United States of America
| | - C. Phoebe Lostroh
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
- * E-mail:
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10
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A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus. ISME JOURNAL 2016; 10:2468-77. [PMID: 27046334 PMCID: PMC5030687 DOI: 10.1038/ismej.2016.34] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 01/05/2016] [Accepted: 02/02/2016] [Indexed: 12/12/2022]
Abstract
The bacterium Myxococcus xanthus glides through soil in search of prey microbes, but when food sources run out, cells cooperatively construct and sporulate within multicellular fruiting bodies. M. xanthus strains isolated from a 16 × 16-cm-scale patch of soil were previously shown to have diversified into many distinct compatibility types that are distinguished by the failure of swarming colonies to merge upon encounter. We sequenced the genomes of 22 isolates from this population belonging to the two most frequently occurring multilocus sequence type (MLST) clades to trace patterns of incipient genomic divergence, specifically related to social divergence. Although homologous recombination occurs frequently within the two MLST clades, we find an almost complete absence of recombination events between them. As the two clades are very closely related and live in sympatry, either ecological or genetic barriers must reduce genetic exchange between them. We find that the rate of change in the accessory genome is greater than the rate of amino-acid substitution in the core genome. We identify a large genomic tract that consistently differs between isolates that do not freely merge and therefore is a candidate region for harbouring gene(s) responsible for self/non-self discrimination.
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Zhu LP, Yue XJ, Han K, Li ZF, Zheng LS, Yi XN, Wang HL, Zhang YM, Li YZ. Allopatric integrations selectively change host transcriptomes, leading to varied expression efficiencies of exotic genes in Myxococcus xanthus. Microb Cell Fact 2015; 14:105. [PMID: 26194479 PMCID: PMC4509775 DOI: 10.1186/s12934-015-0294-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/07/2015] [Indexed: 01/29/2023] Open
Abstract
Background Exotic genes, especially clustered multiple-genes for a complex pathway, are normally integrated into chromosome for heterologous expression. The influences of insertion sites on heterologous expression and allotropic expressions of exotic genes on host remain mostly unclear. Results We compared the integration and expression efficiencies of single and multiple exotic genes that were inserted into Myxococcus xanthus genome by transposition and attB-site-directed recombination. While the site-directed integration had a rather stable chloramphenicol acetyl transferase (CAT) activity, the transposition produced varied CAT enzyme activities. We attempted to integrate the 56-kb gene cluster for the biosynthesis of antitumor polyketides epothilones into M. xanthus genome by site-direction but failed, which was determined to be due to the insertion size limitation at the attB site. The transposition technique produced many recombinants with varied production capabilities of epothilones, which, however, were not paralleled to the transcriptional characteristics of the local sites where the genes were integrated. Comparative transcriptomics analysis demonstrated that the allopatric integrations caused selective changes of host transcriptomes, leading to varied expressions of epothilone genes in different mutants. Conclusions With the increase of insertion fragment size, transposition is a more practicable integration method for the expression of exotic genes. Allopatric integrations selectively change host transcriptomes, which lead to varied expression efficiencies of exotic genes. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0294-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li-Ping Zhu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Xin-Jing Yue
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Kui Han
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Zhi-Feng Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Lian-Shuai Zheng
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Xiu-Nan Yi
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Hai-Long Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - You-Ming Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China.
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Abstract
Many bacteria are naturally competent, able to actively transport environmental DNA fragments across their cell envelope and into their cytoplasm. Because incoming DNA fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular DNA. This review starts with an introductory overview of competence and continues with a detailed consideration of the DNA uptake specificity of competent proteobacteria in the Pasteurellaceae and Neisseriaceae. Species in these distantly related families exhibit strong preferences for genomic DNA from close relatives, a self-specificity arising from the combined effects of biases in the uptake machinery and genomic overrepresentation of the sequences this machinery prefers. Other competent species tested lack obvious uptake bias or uptake sequences, suggesting that strong convergent evolutionary forces have acted on these two families. Recent results show that uptake sequences have multiple "dialects," with clades within each family preferring distinct sequence variants and having corresponding variants enriched in their genomes. Although the genomic consensus uptake sequences are 12 and 29 to 34 bp, uptake assays have found that only central cores of 3 to 4 bp, conserved across dialects, are crucial for uptake. The other bases, which differ between dialects, make weaker individual contributions but have important cooperative interactions. Together, these results make predictions about the mechanism of DNA uptake across the outer membrane, supporting a model for the evolutionary accumulation and stability of uptake sequences and suggesting that uptake biases may be more widespread than currently thought.
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Tan Z, Li H, Pan H, Zhou X, Liu X, Luo N, Hu W, Li Y. Characterization of four type IV pilin homologues in Stigmatella aurantiaca DSM17044 by heterologous expression in Myxococcus xanthus. PLoS One 2013; 8:e75105. [PMID: 24058653 PMCID: PMC3776727 DOI: 10.1371/journal.pone.0075105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 08/09/2013] [Indexed: 11/19/2022] Open
Abstract
As prokaryotic models for multicellular development, Stigmatella aurantiaca and Myxococcus xanthus share many similarities in terms of social behaviors, such as gliding motility. Our current understanding of myxobacterial grouped-cell motilities comes mainly from the research on M. xanthus, which shows that filamentous type IV pili (TFP), composed of type IV pilin (also called PilA protein) subunits, are the key apparatus for social motility (S-motility). However, little is known about the pilin protein in S. aurantiaca. We cloned and sequenced four genes (pilA(Sa1~4)) from S. aurantiaca DSM17044 that are homologous to pilA(Mx) (pilA gene in M. xanthus DK1622). The homology and similarities among pilA(Sa) proteins and other myxobacterial homologues were systematically analyzed. To determine their potential biological functions, the four pilA(Sa) genes were expressed in M. xanthus DK10410 (ΔpilA(Mx)), which did not restore S-motility on soft agar or EPS production to host cells. After further analysis of the motile behaviors in a methylcellulose solution, the M. xanthus strains were categorized into three types. YL6101, carrying pilA(Sa1), and YL6104, carrying pilA(Sa4), produced stable but unretractable surface pili; YL6102, carrying pilA(Sa2), produced stable surface pili and exhibited reduced TFP-dependent motility in methylcellulose; YL6103, carrying pilA(Sa3), produced unstable surface pili. Based on these findings, we propose that pilA(Sa2) might be responsible for the type IV pilin production involved in group motility in S. aurantiaca DSM17044. After examining the developmental processes, it was suggested that the expression of PilA(Sa4) protein might have positive effects on the fruiting body formation of M. xanthus DK10410 cells. Moreover, the formation of fruiting body in M. xanthus cells with stable exogenous TFPSa were compensated by mixing them with S. aurantiaca DSM17044 cells. Our results shed some light on the features and functions of type IV pilin homologues in S. aurantiaca.
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Affiliation(s)
- Zaigao Tan
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Haoming Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Hongwei Pan
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Xiuwen Zhou
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Xin Liu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Ningning Luo
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
- * E-mail:
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
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Hu W, Li L, Sharma S, Wang J, McHardy I, Lux R, Yang Z, He X, Gimzewski JK, Li Y, Shi W. DNA builds and strengthens the extracellular matrix in Myxococcus xanthus biofilms by interacting with exopolysaccharides. PLoS One 2012; 7:e51905. [PMID: 23300576 PMCID: PMC3530553 DOI: 10.1371/journal.pone.0051905] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 11/07/2012] [Indexed: 11/19/2022] Open
Abstract
One intriguing discovery in modern microbiology is the extensive presence of extracellular DNA (eDNA) within biofilms of various bacterial species. Although several biological functions have been suggested for eDNA, including involvement in biofilm formation, the detailed mechanism of eDNA integration into biofilm architecture is still poorly understood. In the biofilms formed by Myxococcus xanthus, a Gram-negative soil bacterium with complex morphogenesis and social behaviors, DNA was found within both extracted and native extracellular matrices (ECM). Further examination revealed that these eDNA molecules formed well organized structures that were similar in appearance to the organization of exopolysaccharides (EPS) in ECM. Biochemical and image analyses confirmed that eDNA bound to and colocalized with EPS within the ECM of starvation biofilms and fruiting bodies. In addition, ECM containing eDNA exhibited greater physical strength and biological stress resistance compared to DNase I treated ECM. Taken together, these findings demonstrate that DNA interacts with EPS and strengthens biofilm structures in M. xanthus.
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Affiliation(s)
- Wei Hu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
- School of Dentistry and Molecular Biology Institute, UCLA, Los Angeles, California, United States of America
| | - Lina Li
- School of Dentistry and Molecular Biology Institute, UCLA, Los Angeles, California, United States of America
| | - Shivani Sharma
- Department of Chemistry and Biochemistry and California NanoSystems Institute (CNSI), UCLA, Los Angeles, California, United States of America
| | - Jing Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
- School of Dentistry and Molecular Biology Institute, UCLA, Los Angeles, California, United States of America
| | - Ian McHardy
- School of Dentistry and Molecular Biology Institute, UCLA, Los Angeles, California, United States of America
| | - Renate Lux
- School of Dentistry and Molecular Biology Institute, UCLA, Los Angeles, California, United States of America
| | - Zhe Yang
- School of Dentistry and Molecular Biology Institute, UCLA, Los Angeles, California, United States of America
| | - Xuesong He
- School of Dentistry and Molecular Biology Institute, UCLA, Los Angeles, California, United States of America
| | - James K. Gimzewski
- Department of Chemistry and Biochemistry and California NanoSystems Institute (CNSI), UCLA, Los Angeles, California, United States of America
- International Center for Materials Nanoarchitectonics Satellite (MANA), National Institute for Materials Science (NIMS), Tsukuba, Japan
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Wenyuan Shi
- School of Dentistry and Molecular Biology Institute, UCLA, Los Angeles, California, United States of America
- * E-mail:
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