1
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Kalia VC, Patel SKS, Karthikeyan KK, Jeya M, Kim IW, Lee JK. Manipulating Microbial Cell Morphology for the Sustainable Production of Biopolymers. Polymers (Basel) 2024; 16:410. [PMID: 38337299 DOI: 10.3390/polym16030410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
The total rate of plastic production is anticipated to surpass 1.1 billion tons per year by 2050. Plastic waste is non-biodegradable and accumulates in natural ecosystems. In 2020, the total amount of plastic waste was estimated to be 367 million metric tons, leading to unmanageable waste disposal and environmental pollution issues. Plastics are produced from petroleum and natural gases. Given the limited fossil fuel reserves and the need to circumvent pollution problems, the focus has shifted to biodegradable biopolymers, such as polyhydroxyalkanoates (PHAs), polylactic acid, and polycaprolactone. PHAs are gaining importance because diverse bacteria can produce them as intracellular inclusion bodies using biowastes as feed. A critical component in PHA production is the downstream processing procedures of recovery and purification. In this review, different bioengineering approaches targeted at modifying the cell morphology and synchronizing cell lysis with the biosynthetic cycle are presented for product separation and extraction. Complementing genetic engineering strategies with conventional downstream processes, these approaches are expected to produce PHA sustainably.
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Affiliation(s)
- Vipin C Kalia
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Kugalur K Karthikeyan
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Marimuthu Jeya
- Marine Biotechnology Division, National Institute of Ocean Technology, Chennai 600100, India
| | - In-Won Kim
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
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2
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Ago R, Tahara YO, Yamaguchi H, Saito M, Ito W, Yamasaki K, Kasai T, Okamoto S, Chikada T, Oshima T, Osaka I, Miyata M, Niki H, Shiomi D. Relationship between the Rod complex and peptidoglycan structure in Escherichia coli. Microbiologyopen 2023; 12:e1385. [PMID: 37877652 PMCID: PMC10561026 DOI: 10.1002/mbo3.1385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Peptidoglycan for elongation in Escherichia coli is synthesized by the Rod complex, which includes RodZ. Although various mutant strains of the Rod complex have been isolated, the relationship between the activity of the Rod complex and the overall physical and chemical structures of the peptidoglycan have not been reported. We constructed a RodZ mutant, termed RMR, and analyzed the growth rate, morphology, and other characteristics of cells producing the Rod complexes containing RMR. The growth and morphology of RMR cells were abnormal, and we isolated suppressor mutants from RMR cells. Most of the suppressor mutations were found in components of the Rod complex, suggesting that these suppressor mutations increase the integrity and/or the activity of the Rod complex. We purified peptidoglycan from wild-type, RMR, and suppressor mutant cells and observed their structures in detail. We found that the peptidoglycan purified from RMR cells had many large holes and different compositions of muropeptides from those of WT cells. The Rod complex may be a determinant not only for the whole shape of peptidoglycan but also for its highly dense structure to support the mechanical strength of the cell wall.
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Affiliation(s)
- Risa Ago
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Yuhei O. Tahara
- Graduate School of ScienceOsaka Metropolitan UniversityOsakaJapan
- The OMU Advanced Research Center for Natural Science and TechnologyOsaka Metropolitan UniversityOsakaJapan
| | - Honoka Yamaguchi
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Motoya Saito
- Department of Biotechnology, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Wakana Ito
- Department of Biotechnology, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Kaito Yamasaki
- Department of Pharmaceutical Engineering, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Taishi Kasai
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Sho Okamoto
- Microbial Physiology Laboratory, Department of Gene Function and PhenomicsNational Institute of GeneticsMishimaShizuokaJapan
| | - Taiki Chikada
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
| | - Taku Oshima
- Department of Biotechnology, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Issey Osaka
- Department of Pharmaceutical Engineering, Faculty of EngineeringToyama Prefectural UniversityImizuToyamaJapan
| | - Makoto Miyata
- Graduate School of ScienceOsaka Metropolitan UniversityOsakaJapan
- The OMU Advanced Research Center for Natural Science and TechnologyOsaka Metropolitan UniversityOsakaJapan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and PhenomicsNational Institute of GeneticsMishimaShizuokaJapan
- Department of GeneticsThe Graduate University for Advanced Studies, SOKENDAIMishimaShizuokaJapan
| | - Daisuke Shiomi
- Department of Life Science, College of ScienceRikkyo UniversityTokyoJapan
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3
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Shlosman I, Fivenson EM, Gilman MSA, Sisley TA, Walker S, Bernhardt TG, Kruse AC, Loparo JJ. Allosteric activation of cell wall synthesis during bacterial growth. Nat Commun 2023; 14:3439. [PMID: 37301887 PMCID: PMC10257715 DOI: 10.1038/s41467-023-39037-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
The peptidoglycan (PG) cell wall protects bacteria against osmotic lysis and determines cell shape, making this structure a key antibiotic target. Peptidoglycan is a polymer of glycan chains connected by peptide crosslinks, and its synthesis requires precise spatiotemporal coordination between glycan polymerization and crosslinking. However, the molecular mechanism by which these reactions are initiated and coupled is unclear. Here we use single-molecule FRET and cryo-EM to show that an essential PG synthase (RodA-PBP2) responsible for bacterial elongation undergoes dynamic exchange between closed and open states. Structural opening couples the activation of polymerization and crosslinking and is essential in vivo. Given the high conservation of this family of synthases, the opening motion that we uncovered likely represents a conserved regulatory mechanism that controls the activation of PG synthesis during other cellular processes, including cell division.
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Affiliation(s)
- Irina Shlosman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Elayne M Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Morgan S A Gilman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Tyler A Sisley
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
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4
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Lamanna MM, Manzoor I, Joseph M, Ye ZA, Benedet M, Zanardi A, Ren Z, Wang X, Massidda O, Tsui HT, Winkler ME. Roles of RodZ and class A PBP1b in the assembly and regulation of the peripheral peptidoglycan elongasome in ovoid-shaped cells of Streptococcus pneumoniae D39. Mol Microbiol 2022; 118:336-368. [PMID: 36001060 PMCID: PMC9804626 DOI: 10.1111/mmi.14969] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 01/17/2023]
Abstract
RodZ of rod-shaped bacteria functions to link MreB filaments to the Rod peptidoglycan (PG) synthase complex that moves circumferentially perpendicular to the long cell axis, creating hoop-like sidewall PG. Ovoid-shaped bacteria, such as Streptococcus pneumoniae (pneumococcus; Spn) that lack MreB, use a different modality for peripheral PG elongation that emanates from the midcell of dividing cells. Yet, S. pneumoniae encodes a RodZ homolog similar to RodZ in rod-shaped bacteria. We show here that the helix-turn-helix and transmembrane domains of RodZ(Spn) are essential for growth at 37°C. ΔrodZ mutations are suppressed by Δpbp1a, mpgA(Y488D), and ΔkhpA mutations that suppress ΔmreC, but not ΔcozE. Consistent with a role in PG elongation, RodZ(Spn) co-localizes with MreC and aPBP1a throughout the cell cycle and forms complexes and interacts with PG elongasome proteins and regulators. Depletion of RodZ(Spn) results in aberrantly shaped, non-growing cells and mislocalization of elongasome proteins MreC, PBP2b, and RodA. Moreover, Tn-seq reveals that RodZ(Spn), but not MreCD(Spn), displays a specific synthetic-viable genetic relationship with aPBP1b, whose function is unknown. We conclude that RodZ(Spn) acts as a scaffolding protein required for elongasome assembly and function and that aPBP1b, like aPBP1a, plays a role in elongasome regulation and possibly peripheral PG synthesis.
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Affiliation(s)
- Melissa M. Lamanna
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Irfan Manzoor
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Merrin Joseph
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Ziyun A. Ye
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Mattia Benedet
- Department of Cellular, Computational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Alessia Zanardi
- Department of Cellular, Computational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Zhongqing Ren
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Xindan Wang
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Orietta Massidda
- Department of Cellular, Computational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Ho‐Ching T. Tsui
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
| | - Malcolm E. Winkler
- Department of BiologyIndiana University BloomingtonBloomingtonIndianaUSA
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5
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Khan F, Jeong GJ, Tabassum N, Mishra A, Kim YM. Filamentous morphology of bacterial pathogens: regulatory factors and control strategies. Appl Microbiol Biotechnol 2022; 106:5835-5862. [PMID: 35989330 DOI: 10.1007/s00253-022-12128-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/03/2022] [Accepted: 08/06/2022] [Indexed: 11/24/2022]
Abstract
Several studies have demonstrated that when exposed to physical, chemical, and biological stresses in the environment, many bacteria (Gram-positive and Gram-negative) change their morphology from a normal cell to a filamentous shape. The formation of filamentous morphology is one of the survival strategies against environmental stress and protection against phagocytosis or protist predators. Numerous pathogenic bacteria have shown filamentous morphologies when examined in vivo or in vitro. During infection, certain pathogenic bacteria adopt a filamentous shape inside the cell to avoid phagocytosis by immune cells. Filamentous morphology has also been seen in biofilms formed on biotic or abiotic surfaces by certain bacteria. As a result, in addition to protecting against phagocytosis by immune cells or predators, the filamentous shape aids in biofilm adhesion or colonization to biotic or abiotic surfaces. Furthermore, these filamentous morphologies of bacterial pathogens lead to antimicrobial drug resistance. Clinically, filamentous morphology has become one of the most serious challenges in treating bacterial infection. The current review went into great detail about the various factors involved in the change of filamentous morphology and the underlying mechanisms. In addition, the review discussed a control strategy for suppressing filamentous morphology in order to combat bacterial infections. Understanding the mechanism underlying the filamentous morphology induced by various environmental conditions will aid in drug development and lessen the virulence of bacterial pathogens. KEY POINTS: • The bacterial filamentation morphology is one of the survival mechanisms against several environmental stress conditions and protection from phagocytosis by host cells and protist predators. • The filamentous morphologies in bacterial pathogens contribute to enhanced biofilm formation, which develops resistance properties against antimicrobial drugs. • Filamentous morphology has become one of the major hurdles in treating bacterial infection, hence controlling strategies employed for inhibiting the filamentation morphology from combating bacterial infections.
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Affiliation(s)
- Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea. .,Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, Republic of Korea.
| | - Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Nazia Tabassum
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, 48513, Republic of Korea
| | - Akanksha Mishra
- Department of Biotechnology, Division of Research and Development, Lovely Professional University, Phagwara, Punjab, 144001, India
| | - Young-Mog Kim
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea. .,Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, Republic of Korea. .,Department of Food Science and Technology, Pukyong National University, Busan, 48513, Republic of Korea.
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6
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Li M, Zhang J, Bai Q, Fang L, Song H, Cao Y. Non-homologous End Joining-Mediated Insertional Mutagenesis Reveals a Novel Target for Enhancing Fatty Alcohols Production in Yarrowia lipolytica. Front Microbiol 2022; 13:898884. [PMID: 35547152 PMCID: PMC9082995 DOI: 10.3389/fmicb.2022.898884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Non-homologous end joining (NHEJ)-mediated integration is effective in generating random mutagenesis to identify beneficial gene targets in the whole genome, which can significantly promote the performance of the strains. Here, a novel target leading to higher protein synthesis was identified by NHEJ-mediated integration that seriously improved fatty alcohols biosynthesis in Yarrowia lipolytica. One batch of strains transformed with fatty acyl-CoA reductase gene (FAR) showed significant differences (up to 70.53-fold) in fatty alcohol production. Whole-genome sequencing of the high-yield strain demonstrated that a new target YALI0_A00913g ("A1 gene") was disrupted by NHEJ-mediated integration of partial carrier DNA, and reverse engineering of the A1 gene disruption (YlΔA1-FAR) recovered the fatty alcohol overproduction phenotype. Transcriptome analysis of YlΔA1-FAR strain revealed A1 disruption led to strengthened protein synthesis process that was confirmed by sfGFP gene expression, which may account for enhanced cell viability and improved biosynthesis of fatty alcohols. This study identified a novel target that facilitated synthesis capacity and provided new insights into unlocking biosynthetic potential for future genetic engineering in Y. lipolytica.
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Affiliation(s)
- Mengxu Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Jinlai Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Qiuyan Bai
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Lixia Fang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
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7
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Graham CLB, Newman H, Gillett FN, Smart K, Briggs N, Banzhaf M, Roper DI. A Dynamic Network of Proteins Facilitate Cell Envelope Biogenesis in Gram-Negative Bacteria. Int J Mol Sci 2021; 22:12831. [PMID: 34884635 PMCID: PMC8657477 DOI: 10.3390/ijms222312831] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 01/01/2023] Open
Abstract
Bacteria must maintain the ability to modify and repair the peptidoglycan layer without jeopardising its essential functions in cell shape, cellular integrity and intermolecular interactions. A range of new experimental techniques is bringing an advanced understanding of how bacteria regulate and achieve peptidoglycan synthesis, particularly in respect of the central role played by complexes of Sporulation, Elongation or Division (SEDs) and class B penicillin-binding proteins required for cell division, growth and shape. In this review we highlight relationships implicated by a bioinformatic approach between the outer membrane, cytoskeletal components, periplasmic control proteins, and cell elongation/division proteins to provide further perspective on the interactions of these cell division, growth and shape complexes. We detail the network of protein interactions that assist in the formation of peptidoglycan and highlight the increasingly dynamic and connected set of protein machinery and macrostructures that assist in creating the cell envelope layers in Gram-negative bacteria.
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Affiliation(s)
- Chris L. B. Graham
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
| | - Hector Newman
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
| | - Francesca N. Gillett
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - Katie Smart
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
| | - Nicholas Briggs
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
| | - Manuel Banzhaf
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
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8
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FtsA acts through FtsW to promote cell wall synthesis during cell division in Escherichia coli. Proc Natl Acad Sci U S A 2021; 118:2107210118. [PMID: 34453005 DOI: 10.1073/pnas.2107210118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Escherichia coli, FtsQLB is required to recruit the essential septal peptidoglycan (sPG) synthase FtsWI to FtsA, which tethers FtsZ filaments to the membrane. The arrival of FtsN switches FtsQLB in the periplasm and FtsA in the cytoplasm from a recruitment role to active forms that synergize to activate FtsWI. Genetic evidence indicates that the active form of FtsQLB has an altered conformation with an exposed domain of FtsL that acts on FtsI to activate FtsW. However, how FtsA contributes to the activation of FtsW is not clear, as it could promote the conformational change in FtsQLB or act directly on FtsW. Here, we show that the overexpression of an activated FtsA (FtsA*) bypasses FtsQ, indicating it can compensate for FtsQ's recruitment function. Consistent with this, FtsA* also rescued FtsL and FtsB mutants deficient in FtsW recruitment. FtsA* also rescued an FtsL mutant unable to deliver the periplasmic signal from FtsN, consistent with FtsA* acting on FtsW. In support of this, an FtsW mutant was isolated that was rescued by an activated FtsQLB but not by FtsA*, indicating it was specifically defective in activation by FtsA. Our results suggest that in response to FtsN, the active form of FtsA acts on FtsW in the cytoplasm and synergizes with the active form of FtsQLB acting on FtsI in the periplasm to activate FtsWI to carry out sPG synthesis.
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9
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Garner EC. Toward a Mechanistic Understanding of Bacterial Rod Shape Formation and Regulation. Annu Rev Cell Dev Biol 2021; 37:1-21. [PMID: 34186006 DOI: 10.1146/annurev-cellbio-010521-010834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
One of the most common bacterial shapes is a rod, yet we have a limited understanding of how this simple shape is constructed. While only six proteins are required for rod shape, we are just beginning to understand how they self-organize to build the micron-sized enveloping structures that define bacterial shape out of nanometer-sized glycan strains. Here, we detail and summarize the insights gained over the last 20 years into this complex problem that have been achieved with a wide variety of different approaches. We also explain and compare both current and past models of rod shape formation and maintenance and then highlight recent insights into how the Rod complex might be regulated. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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10
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Li Y, Gong H, Zhan R, Ouyang S, Park KT, Lutkenhaus J, Du S. Genetic analysis of the septal peptidoglycan synthase FtsWI complex supports a conserved activation mechanism for SEDS-bPBP complexes. PLoS Genet 2021; 17:e1009366. [PMID: 33857142 PMCID: PMC8078798 DOI: 10.1371/journal.pgen.1009366] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/27/2021] [Accepted: 03/18/2021] [Indexed: 01/22/2023] Open
Abstract
SEDS family peptidoglycan (PG) glycosyltransferases, RodA and FtsW, require their cognate transpeptidases PBP2 and FtsI (class B penicillin binding proteins) to synthesize PG along the cell cylinder and at the septum, respectively. The activities of these SEDS-bPBPs complexes are tightly regulated to ensure proper cell elongation and division. In Escherichia coli FtsN switches FtsA and FtsQLB to the active forms that synergize to stimulate FtsWI, but the exact mechanism is not well understood. Previously, we isolated an activation mutation in ftsW (M269I) that allows cell division with reduced FtsN function. To try to understand the basis for activation we isolated additional substitutions at this position and found that only the original substitution produced an active mutant whereas drastic changes resulted in an inactive mutant. In another approach we isolated suppressors of an inactive FtsL mutant and obtained FtsWE289G and FtsIK211I and found they bypassed FtsN. Epistatic analysis of these mutations and others confirmed that the FtsN-triggered activation signal goes from FtsQLB to FtsI to FtsW. Mapping these mutations, as well as others affecting the activity of FtsWI, on the RodA-PBP2 structure revealed they are located at the interaction interface between the extracellular loop 4 (ECL4) of FtsW and the pedestal domain of FtsI (PBP3). This supports a model in which the interaction between the ECL4 of SEDS proteins and the pedestal domain of their cognate bPBPs plays a critical role in the activation mechanism. Bacterial cell division requires the synthesis of septal peptidoglycan by the widely conserved SEDS-bPBP protein complex FtsWI, but how the complex is activated during cell division is still poorly understood. Previous studies suggested that FtsN initiates a signaling cascade in the periplasm to activate FtsWI. Here we isolated and characterized activated FtsW and FtsI mutants and confirmed that the signaling cascade for FtsW activation goes from FtsN to FtsQLB to FtsI and then to FtsW. The residues corresponding to mutations affecting FtsWI activation are clustered to a small region of the interaction interface between the pedestal domain of FtsI and the extracellular loop 4 of FtsW, suggesting that this interaction mediates activation of FtsW. This is strikingly similar to the proposed activation mechanism for the RodA-PBP2 complex, another SEDS-bPBP complex required for cell elongation. Thus, the two homologous SEDS-bPBP complexes are activated similarly by completely unrelated activators that modulate the interaction interface between the SEDS proteins and the bPBPs.
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Affiliation(s)
- Ying Li
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, HB, China
| | - Han Gong
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, HB, China
| | - Rui Zhan
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, HB, China
| | - Shushan Ouyang
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, HB, China
| | - Kyung-Tae Park
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Joe Lutkenhaus
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, United States of America
- * E-mail: (JL); (SD)
| | - Shishen Du
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, HB, China
- * E-mail: (JL); (SD)
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11
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The BB0345 Hypothetical Protein of Borrelia burgdorferi Is Essential for Mammalian Infection. Infect Immun 2020; 88:IAI.00472-20. [PMID: 32928963 DOI: 10.1128/iai.00472-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022] Open
Abstract
During the natural enzootic life cycle of Borrelia burgdorferi (also known as Borreliella burgdorferi), the bacteria must sense conditions within the vertebrate and arthropod and appropriately regulate expression of genes necessary to persist within these distinct environments. bb0345 of B. burgdorferi encodes a hypothetical protein of unknown function that is predicted to contain an N-terminal helix-turn-helix (HTH) domain. Because HTH domains can mediate protein-DNA interactions, we hypothesized that BB0345 might represent a previously unidentified borrelial transcriptional regulator with the ability to regulate events critical for the B. burgdorferi enzootic cycle. To study the role of BB0345 within mammals, we generated a bb0345 mutant and assessed its virulence potential in immunocompetent mice. The bb0345 mutant was able to initiate localized infection and disseminate to distal tissues but was cleared from all sites by 14 days postinfection. In vitro growth curve analyses revealed that the bb0345 mutant grew similar to wild-type bacteria in standard Barbour-Stoenner-Kelley II (BSK-II) medium; however, the mutant was not able to grow in dilute BSK-II medium or dialysis membrane chambers (DMCs) implanted in rats. Proteinase K accessibility assays and whole-cell partitioning indicated that BB0345 was intracellular and partially membrane associated. Comparison of protein production profiles between the wild-type parent and the bb0345 mutant revealed no major differences, suggesting BB0345 may not be a global transcriptional regulator. Taken together, these data show that BB0345 is essential for B. burgdorferi survival in the mammalian host, potentially by aiding the spirochete with a physiological function that is required by the bacterium during infection.
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Ding Q, Diao W, Gao C, Chen X, Liu L. Microbial cell engineering to improve cellular synthetic capacity. Biotechnol Adv 2020; 45:107649. [PMID: 33091485 DOI: 10.1016/j.biotechadv.2020.107649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/02/2020] [Accepted: 10/13/2020] [Indexed: 01/21/2023]
Abstract
Rapid technological progress in gene assembly, biosensors, and genetic circuits has led to reinforce the cellular synthetic capacity for chemical production. However, overcoming the current limitations of these techniques in maintaining cellular functions and enhancing the cellular synthetic capacity (e.g., catalytic efficiency, strain performance, and cell-cell communication) remains challenging. In this review, we propose a strategy for microbial cell engineering to improve the cellular synthetic capacity by utilizing biotechnological tools along with system biology methods to regulate cellular functions during chemical production. Current strategies in microbial cell engineering are mainly focused on the organelle, cell, and consortium levels. This review highlights the potential of using biotechnology to further develop the field of microbial cell engineering and provides guidance for utilizing microorganisms as attractive regulation targets.
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Affiliation(s)
- Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wenwen Diao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
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13
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Morphology engineering: a new strategy to construct microbial cell factories. World J Microbiol Biotechnol 2020; 36:127. [PMID: 32712725 DOI: 10.1007/s11274-020-02903-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/14/2020] [Indexed: 10/23/2022]
Abstract
Currently, synthetic biology approaches have been developed for constructing microbial cell factories capable of efficient synthesis of high value-added products. Most studies have focused on the construction of novel biosynthetic pathways and their regulatory processes. Morphology engineering has recently been proposed as a novel strategy for constructing efficient microbial cell factories, which aims at controlling cell shape and cell division pattern by manipulating the cell morphology-related genes. Morphology engineering strategies have been exploited for improving bacterial growth rate, enlarging cell volume and simplifying downstream separation. This mini-review summarizes cell morphology-related proteins and their function, current advances in manipulation tools and strategies of morphology engineering, and practical applications of morphology engineering for enhanced production of intracellular product polyhydroxyalkanoate and extracellular products. Furthermore, current limitations and the future development direction using morphology engineering are proposed.
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14
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Regulation of filamentation by bacteria and its impact on the productivity of compounds in biotechnological processes. Appl Microbiol Biotechnol 2020; 104:4631-4642. [DOI: 10.1007/s00253-020-10590-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 12/29/2022]
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15
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Shi H, Quint DA, Grason GM, Gopinathan A, Huang KC. Chiral twisting in a bacterial cytoskeletal polymer affects filament size and orientation. Nat Commun 2020; 11:1408. [PMID: 32179732 PMCID: PMC7075873 DOI: 10.1038/s41467-020-14752-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/24/2020] [Indexed: 12/30/2022] Open
Abstract
In many rod-shaped bacteria, the actin homolog MreB directs cell-wall insertion and maintains cell shape, but it remains unclear how structural changes to MreB affect its organization in vivo. Here, we perform molecular dynamics simulations for Caulobacter crescentus MreB to extract mechanical parameters for inputs into a coarse-grained biophysical polymer model that successfully predicts MreB filament properties in vivo. Our analyses indicate that MreB double protofilaments can exhibit left-handed twisting that is dependent on the bound nucleotide and membrane binding; the degree of twisting correlates with the length and orientation of MreB filaments observed in vitro and in vivo. Our molecular dynamics simulations also suggest that membrane binding of MreB double protofilaments induces a stable membrane curvature of similar magnitude to that observed in vivo. Thus, our multiscale modeling correlates cytoskeletal filament size with conformational changes inferred from molecular dynamics simulations, providing a paradigm for connecting protein filament structure and mechanics to cellular organization and function. The actin homolog MreB directs cell-wall insertion and maintains cell shape in many rod-shaped bacteria. Here, Shi et al. perform molecular dynamics simulations for MreB to extract mechanical parameters for inputs into a coarse-grained biophysical polymer model that predicts MreB filament properties.
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Affiliation(s)
- Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - David A Quint
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Department of Physics, University of California at Merced, Merced, CA, 95343, USA.,NSF-CREST: Center for Cellular and Biomolecular Machines, University of California at Merced, Merced, CA, 95343, USA
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA, 01003, USA
| | - Ajay Gopinathan
- Department of Physics, University of California at Merced, Merced, CA, 95343, USA.,NSF-CREST: Center for Cellular and Biomolecular Machines, University of California at Merced, Merced, CA, 95343, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. .,Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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16
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Superstructure formation by RodZ hexamers of Shigella sonnei maintains the rod shape of bacilli. PLoS One 2020; 15:e0228052. [PMID: 32053625 PMCID: PMC7018016 DOI: 10.1371/journal.pone.0228052] [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: 08/22/2019] [Accepted: 01/06/2020] [Indexed: 11/19/2022] Open
Abstract
The rod shape of bacilli is maintained by bacterial cytoskeletal protein MreB, an actin homolog that acts in concert with the inner membrane protein RodZ. We previously reported RodZ binds RNA to control the posttranscriptional regulation of invE (virB), which controls the type III secretion system essential for the virulence of Shigella. Here, we show that purified RodZ forms "superstructures" of high molecular mass that dissociate into a midsized "basal complex" in the presence of nonionic detergent, or to a monomer in the presence of dithiothreitol. We used mass spectrometry to show that the basal complex was a hexamer. Electrophoresis mobility shift assays combined with gel filtration detected the RNA-binding activity in fractions containing molecules larger than the basal hexamer. The superstructure was consistently detected with MreB in crude cell lysates of S. sonnei that were fractionated using gel filtration. Immunofluorescence microscopy using two different super-resolution settings showed that wild-type RodZ was distributed in cells as separate dots. Consistent with the superstructure comprising homohexamers, majority of the dots distributed among areas of discrete values. In addition, simultaneous immunodetection of MreB provided the first evidence of colocalization with RodZ as larger patch like signals. These findings indicate that native RodZ forms clusters of various sizes, which may correspond to a superstructure comprising multiple hexamers required for the RNA-binding activity.
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17
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Burt A, Cassidy CK, Ames P, Bacia-Verloop M, Baulard M, Huard K, Luthey-Schulten Z, Desfosses A, Stansfeld PJ, Margolin W, Parkinson JS, Gutsche I. Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain. Nat Commun 2020; 11:743. [PMID: 32029744 PMCID: PMC7005262 DOI: 10.1038/s41467-020-14350-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/21/2019] [Indexed: 12/01/2022] Open
Abstract
Motile bacteria sense chemical gradients with transmembrane receptors organised in supramolecular signalling arrays. Understanding stimulus detection and transmission at the molecular level requires precise structural characterisation of the array building block known as a core signalling unit. Here we introduce an Escherichia coli strain that forms small minicells possessing extended and highly ordered chemosensory arrays. We use cryo-electron tomography and subtomogram averaging to provide a three-dimensional map of a complete core signalling unit, with visible densities corresponding to the HAMP and periplasmic domains. This map, combined with previously determined high resolution structures and molecular dynamics simulations, yields a molecular model of the transmembrane core signalling unit and enables spatial localisation of its individual domains. Our work thus offers a solid structural basis for the interpretation of a wide range of existing data and the design of further experiments to elucidate signalling mechanisms within the core signalling unit and larger array.
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Affiliation(s)
- Alister Burt
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Peter Ames
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Maria Bacia-Verloop
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Megghane Baulard
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Karine Huard
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - William Margolin
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - John S Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France.
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18
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Awuni E. Status of Targeting MreB for the Development of Antibiotics. Front Chem 2020; 7:884. [PMID: 31998684 PMCID: PMC6965359 DOI: 10.3389/fchem.2019.00884] [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: 10/02/2019] [Accepted: 12/06/2019] [Indexed: 12/15/2022] Open
Abstract
Although many prospective antibiotic targets are known, bacterial infections and resistance to antibiotics remain a threat to public health partly because the druggable potentials of most of these targets have yet to be fully tapped for the development of a new generation of therapeutics. The prokaryotic actin homolog MreB is one of the important antibiotic targets that are yet to be significantly exploited. MreB is a bacterial cytoskeleton protein that has been widely studied and is associated with the determination of rod shape as well as important subcellular processes including cell division, chromosome segregation, cell wall morphogenesis, and cell polarity. Notwithstanding that MreB is vital and conserved in most rod-shaped bacteria, no approved antibiotics targeting it are presently available. Here, the status of targeting MreB for the development of antibiotics is concisely summarized. Expressly, the known therapeutic targets and inhibitors of MreB are presented, and the way forward in the search for a new generation of potent inhibitors of MreB briefly discussed.
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Affiliation(s)
- Elvis Awuni
- Department of Biochemistry, School of Biological Sciences, CANS, University of Cape Coast, Cape Coast, Ghana
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19
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Ago R, Shiomi D. RodZ: a key-player in cell elongation and cell division in Escherichia coli. AIMS Microbiol 2019; 5:358-367. [PMID: 31915748 PMCID: PMC6946637 DOI: 10.3934/microbiol.2019.4.358] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/06/2019] [Indexed: 01/08/2023] Open
Abstract
RodZ is required for determination of cell shape in rod-shaped bacterium, such as Escherichia coli. RodZ is a transmembrane protein and forms a supramolecular complex called the Rod complex with other proteins, such as MreB-actin and peptidoglycan synthesis enzymes (for e.g., PBP2). Deletion of the rodZ gene changes the cell shape from rod to round or ovoid. Another supramolecular complex called divisome that controls cell division mainly consists of FtsZ-tubulin. MreB directly interacts with FtsZ and this interaction is critical to trigger a transition from cell elongation to cell division. Recently, we found that RodZ also directly interacts with FtsZ, and RodZ recruits MreB to the divisome. Formation of the division ring, called Z ring, is delayed if RodZ does not interact with FtsZ, indicating that RodZ might facilitate the formation of the Z ring during the cell division process. In this mini-review, we have summarized the roles of RodZ in cell elongation and cell division, especially based on our recent study.
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Affiliation(s)
- Risa Ago
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Daisuke Shiomi
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
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20
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Dong LJ, Lai YJ, Yu SJ, Liu JF. Speciation Analysis of the Uptake and Biodistribution of Nanoparticulate and Ionic Silver in Escherichia coli. Anal Chem 2019; 91:12525-12530. [DOI: 10.1021/acs.analchem.9b03359] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Li-Jie Dong
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu-Jian Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Su-Juan Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
| | - Jing-Fu Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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21
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Ruhe ZC, Subramanian P, Song K, Nguyen JY, Stevens TA, Low DA, Jensen GJ, Hayes CS. Programmed Secretion Arrest and Receptor-Triggered Toxin Export during Antibacterial Contact-Dependent Growth Inhibition. Cell 2019; 175:921-933.e14. [PMID: 30388452 DOI: 10.1016/j.cell.2018.10.033] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/31/2018] [Accepted: 09/05/2018] [Indexed: 12/21/2022]
Abstract
Contact-dependent growth inhibition (CDI) entails receptor-mediated delivery of CdiA-derived toxins into Gram-negative target bacteria. Using electron cryotomography, we show that each CdiA effector protein forms a filament extending ∼33 nm from the cell surface. Remarkably, the extracellular filament represents only the N-terminal half of the effector. A programmed secretion arrest sequesters the C-terminal half of CdiA, including the toxin domain, in the periplasm prior to target-cell recognition. Upon binding receptor, CdiA secretion resumes, and the periplasmic FHA-2 domain is transferred to the target-cell outer membrane. The C-terminal toxin region of CdiA then penetrates into the target-cell periplasm, where it is cleaved for subsequent translocation into the cytoplasm. Our findings suggest that the FHA-2 domain assembles into a transmembrane conduit for toxin transport into the periplasm of target bacteria. We propose that receptor-triggered secretion ensures that FHA-2 export is closely coordinated with integration into the target-cell outer membrane. VIDEO ABSTRACT.
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Affiliation(s)
- Zachary C Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Poorna Subramanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kiho Song
- Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Josephine Y Nguyen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Taylor A Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA.
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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22
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Yoshii Y, Niki H, Shiomi D. Division-site localization of RodZ is required for efficient Z ring formation in Escherichia coli. Mol Microbiol 2019; 111:1229-1244. [PMID: 30742332 DOI: 10.1111/mmi.14217] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2019] [Indexed: 12/25/2022]
Abstract
Bacteria such as Escherichia coli must coordinate cell elongation and cell division. Elongation is regulated by an elongasome complex containing MreB actin and the transmembrane protein RodZ, which regulates assembly of MreB, whereas division is regulated by a divisome complex containing FtsZ tubulin. These complexes were previously thought to function separately. However, MreB has been shown to directly interact with FtsZ to switch to cell division from cell elongation, indicating that these complexes collaborate to regulate both processes. Here, we investigated the role of RodZ in the regulation of cell division. RodZ localized to the division site in an FtsZ-dependent manner. We also found that division-site localization of MreB was dependent on RodZ. Formation of a Z ring was delayed by deletion of rodZ, suggesting that division-site localization of RodZ facilitated the formation or stabilization of the Z ring during early cell division. Thus, RodZ functions to regulate MreB assembly during cell elongation and facilitates the formation of the Z ring during cell division in E. coli.
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Affiliation(s)
- Yusuke Yoshii
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Daisuke Shiomi
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
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23
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Yang H, Wang F, Wang H, Lu X, Shen W, Chen X. Deleting mrdA and mrcB to significantly improve extracellular recombinant protein production in Escherichia coli. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Shi H, Bratton BP, Gitai Z, Huang KC. How to Build a Bacterial Cell: MreB as the Foreman of E. coli Construction. Cell 2019. [PMID: 29522748 DOI: 10.1016/j.cell.2018.02.050] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cell shape matters across the kingdoms of life, and cells have the remarkable capacity to define and maintain specific shapes and sizes. But how are the shapes of micron-sized cells determined from the coordinated activities of nanometer-sized proteins? Here, we review general principles that have surfaced through the study of rod-shaped bacterial growth. Imaging approaches have revealed that polymers of the actin homolog MreB play a central role. MreB both senses and changes cell shape, thereby generating a self-organizing feedback system for shape maintenance. At the molecular level, structural and computational studies indicate that MreB filaments exhibit tunable mechanical properties that explain their preference for certain geometries and orientations along the cylindrical cell body. We illustrate the regulatory landscape of rod-shape formation and the connectivity between cell shape, cell growth, and other aspects of cell physiology. These discoveries provide a framework for future investigations into the architecture and construction of microbes.
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Affiliation(s)
- Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Benjamin P Bratton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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25
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Kurita K, Shin R, Tabei T, Shiomi D. Relation between rotation of MreB actin and cell width of Escherichia coli. Genes Cells 2019; 24:259-265. [PMID: 30597729 DOI: 10.1111/gtc.12667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 12/25/2018] [Accepted: 12/26/2018] [Indexed: 12/27/2022]
Abstract
Bacterial cells, including Escherichia coli and Bacillus subtilis, continuously elongate and divide. Although the cell width is maintained during cell cycle, the molecular mechanisms involved in its regulation remain unknown. MreB has been implicated to play a role in maintaining cell width. Several point mutations in mreB that affect cell width have been identified. The MreB protein forms clusters or polymers in the cell and moves along annular tracks perpendicular to the long axis. This rotation is coupled with peptidoglycan synthesis. Here, we focused on two MreB mutants, MreBA125V and MreBA174T . Cells producing MreBA125V and MreBA174T were thinner and thicker than WT cells, and MreBA125V and MreBA174T rotated faster and slower than WT MreB, respectively. We observed that the rotation rate correlated with the cell wall synthesis rate. Thus, we conclude that the velocity of MreB rotation also affects cell width, that is, the faster the MreB rotates, the thinner the cell width is.
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Affiliation(s)
- Keisuke Kurita
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Ryota Shin
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Tsutomu Tabei
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Daisuke Shiomi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
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26
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Rohs PDA, Buss J, Sim SI, Squyres GR, Srisuknimit V, Smith M, Cho H, Sjodt M, Kruse AC, Garner EC, Walker S, Kahne DE, Bernhardt TG. A central role for PBP2 in the activation of peptidoglycan polymerization by the bacterial cell elongation machinery. PLoS Genet 2018; 14:e1007726. [PMID: 30335755 PMCID: PMC6207328 DOI: 10.1371/journal.pgen.1007726] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/30/2018] [Accepted: 10/01/2018] [Indexed: 01/13/2023] Open
Abstract
Cell elongation in rod-shaped bacteria is mediated by the Rod system, a conserved morphogenic complex that spatially controls cell wall assembly by the glycan polymerase RodA and crosslinking enzyme PBP2. Using Escherichia coli as a model system, we identified a PBP2 variant that promotes Rod system function when essential accessory components of the machinery are inactivated. This PBP2 variant hyperactivates cell wall synthesis in vivo and stimulates the activity of RodA-PBP2 complexes in vitro. Cells with the activated synthase also exhibited enhanced polymerization of the actin-like MreB component of the Rod system. Our results define an activation pathway governing Rod system function in which PBP2 conformation plays a central role in stimulating both glycan polymerization by its partner RodA and the formation of cytoskeletal filaments of MreB to orient cell wall assembly. In light of these results, previously isolated mutations that activate cytokinesis suggest that an analogous pathway may also control cell wall synthesis by the division machinery.
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Affiliation(s)
- Patricia D. A. Rohs
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jackson Buss
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sue I. Sim
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Georgia R. Squyres
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Veerasak Srisuknimit
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Mandy Smith
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hongbaek Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi, Korea
| | - Megan Sjodt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrew C. Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ethan C. Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniel E. Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Thomas G. Bernhardt
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
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27
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Özdemir B, Asgharzadeh P, Birkhold AI, Mueller SJ, Röhrle O, Reski R. Cytological analysis and structural quantification of FtsZ1-2 and FtsZ2-1 network characteristics in Physcomitrella patens. Sci Rep 2018; 8:11165. [PMID: 30042487 PMCID: PMC6057934 DOI: 10.1038/s41598-018-29284-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/05/2018] [Indexed: 11/24/2022] Open
Abstract
Although the concept of the cytoskeleton as a cell-shape-determining scaffold is well established, it remains enigmatic how eukaryotic organelles adopt and maintain a specific morphology. The Filamentous Temperature Sensitive Z (FtsZ) protein family, an ancient tubulin, generates complex polymer networks, with striking similarity to the cytoskeleton, in the chloroplasts of the moss Physcomitrella patens. Certain members of this protein family are essential for structural integrity and shaping of chloroplasts, while others are not, illustrating the functional diversity within the FtsZ protein family. Here, we apply a combination of confocal laser scanning microscopy and a self-developed semi-automatic computational image analysis method for the quantitative characterisation and comparison of network morphologies and connectivity features for two selected, functionally dissimilar FtsZ isoforms, FtsZ1-2 and FtsZ2-1. We show that FtsZ1-2 and FtsZ2-1 networks are significantly different for 8 out of 25 structural descriptors. Therefore, our results demonstrate that different FtsZ isoforms are capable of generating polymer networks with distinctive morphological and connectivity features which might be linked to the functional differences between the two isoforms. To our knowledge, this is the first study to employ computational algorithms in the quantitative comparison of different classes of protein networks in living cells.
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Affiliation(s)
- Bugra Özdemir
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Pouyan Asgharzadeh
- Institute of Applied Mechanics, University of Stuttgart, Pfaffenwaldring 7, 70569, Stuttgart, Germany
- Stuttgart Center for Simulation Science (SimTech), University of Stuttgart, Pfaffenwaldring 5a, 70569, Stuttgart, Germany
| | - Annette I Birkhold
- Institute of Applied Mechanics, University of Stuttgart, Pfaffenwaldring 7, 70569, Stuttgart, Germany
| | - Stefanie J Mueller
- INRES - Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Oliver Röhrle
- Institute of Applied Mechanics, University of Stuttgart, Pfaffenwaldring 7, 70569, Stuttgart, Germany.
- Stuttgart Center for Simulation Science (SimTech), University of Stuttgart, Pfaffenwaldring 5a, 70569, Stuttgart, Germany.
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany.
- BIOSS - Centre for Biological Signalling Research, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany.
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany.
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28
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Bratton BP, Shaevitz JW, Gitai Z, Morgenstein RM. MreB polymers and curvature localization are enhanced by RodZ and predict E. coli's cylindrical uniformity. Nat Commun 2018; 9:2797. [PMID: 30022070 PMCID: PMC6052060 DOI: 10.1038/s41467-018-05186-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/20/2018] [Indexed: 12/31/2022] Open
Abstract
The actin-like protein MreB has been proposed to coordinate the synthesis of the cell wall to determine cell shape in bacteria. MreB is preferentially localized to areas of the cell with specific curved geometries, avoiding the cell poles. It remains unclear whether MreB’s curvature preference is regulated by additional factors, and which specific features of MreB promote specific features of rod shape growth. Here, we show that the transmembrane protein RodZ modulates MreB curvature preference and polymer number in E. coli, properties which are regulated independently. An unbiased machine learning analysis shows that MreB polymer number, the total length of MreB polymers, and MreB curvature preference are key correlates of cylindrical uniformity, the variability in radius within a single cell. Changes in the values of these parameters are highly predictive of the resulting changes in cell shape (r2 = 0.93). Our data thus suggest RodZ promotes the assembly of geometrically-localized MreB polymers that lead to the growth of uniform cylinders. The actin-like protein MreB coordinates the synthesis of the cell wall, which determines cell shape in bacteria. Here, Bratton et al. show that the transmembrane protein RodZ modulates MreB polymer number and curvature preference, contributing to the cylindrical uniform shape of E. coli cells.
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Affiliation(s)
- Benjamin P Bratton
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Department of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Joshua W Shaevitz
- Department of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
| | - Randy M Morgenstein
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA. .,Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA.
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29
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Xiao-Ran J, Jin Y, Xiangbin C, Guo-Qiang C. Halomonas and Pathway Engineering for Bioplastics Production. Methods Enzymol 2018; 608:309-328. [PMID: 30173767 DOI: 10.1016/bs.mie.2018.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Traditional microbial chassis, including Escherichia coli, Bacillus subtilis, Ralstonia eutropha, and Pseudomonas putida, are grown under neutral pH and mild osmotic pressure for production of chemicals and materials. They tend to be contaminated easily by many microorganisms. To address this issue, next-generation industrial biotechnology employing halophilic Halomonas spp. has been developed for production of bioplastics polyhydroxyalkanoates (PHAs) and other chemicals. Halomonas spp. that can be grown contamination free under open and unsterile condition at alkali pH and high NaCl have been engineered to produce several PHA polymers in elongated or enlarged cells. New pathways can also be constructed both in plasmids and on chromosomes for Halomonas spp. Synthetic biology approaches and parts have been developed for Halomonas spp., allowing better control of their growth and product formation as well as morphology adjustment. Halomonas spp. and their synthetic biology will play an increasingly important role for industrial production of large volume chemicals.
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Affiliation(s)
- Jiang Xiao-Ran
- MOE Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yin Jin
- MOE Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Chen Xiangbin
- MOE Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Chen Guo-Qiang
- MOE Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China; Manchester Institute of Biotechnology, Centre for Synthetic Biology, The University of Manchester, Manchester, United Kingdom.
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30
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RodZ modulates geometric localization of the bacterial actin MreB to regulate cell shape. Nat Commun 2018; 9:1280. [PMID: 29599448 PMCID: PMC5876373 DOI: 10.1038/s41467-018-03633-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/01/2018] [Indexed: 01/10/2023] Open
Abstract
In the rod-shaped bacterium Escherichia coli, the actin-like protein MreB localizes in a curvature-dependent manner and spatially coordinates cell-wall insertion to maintain cell shape, although the molecular mechanism by which cell width is regulated remains unknown. Here we demonstrate that the membrane protein RodZ regulates the biophysical properties of MreB and alters the spatial organization of E. coli cell-wall growth. The relative expression levels of MreB and RodZ change in a manner commensurate with variations in growth rate and cell width, and RodZ systematically alters the curvature-based localization of MreB and cell width in a concentration-dependent manner. We identify MreB mutants that alter the bending properties of MreB filaments in molecular dynamics simulations similar to RodZ binding, and show that these mutants rescue rod-like shape in the absence of RodZ alone or in combination with wild-type MreB. Thus, E. coli can control its shape and dimensions by differentially regulating RodZ and MreB to alter the patterning of cell-wall insertion, highlighting the rich regulatory landscape of cytoskeletal molecular biophysics. Membrane protein RodZ interacts with the actin-like protein MreB, which coordinates cell-wall insertion to maintain the typical rod-like shape of E. coli cells. Here, the authors provide evidence that RodZ modulates the biophysical properties of MreB and alters the spatial organization of cell-wall growth.
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31
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Ikebe R, Kuwabara Y, Chikada T, Niki H, Shiomi D. The periplasmic disordered domain of RodZ promotes its self-interaction in Escherichia coli. Genes Cells 2018; 23:307-317. [PMID: 29480545 DOI: 10.1111/gtc.12572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 01/24/2018] [Indexed: 11/28/2022]
Abstract
Rod shape of bacterial cells such as Escherichia coli is mainly regulated by a supramolecular complex called elongasome including MreB actin. Deletion of the mreB gene in rod-shaped bacterium E. coli results in round-shaped cells. RodZ was isolated as a determinant of rod shape in E. coli, Caulobacter crescentus and Bacillus subtilis and it has been shown to be an interaction partner and a regulator of assembly of MreB through its cytoplasmic domain. As opposed to functions of the N-terminal cytoplasmic domain of RodZ, functions of the C-terminal periplasmic domain including a disordered region are still unclear. To understand it, we adopted an in vivo photo-cross-linking assay to analyze interaction partners to identify proteins which interact with RodZ via its periplasmic domain, finding that the RodZ self-interacts in the periplasmic disordered domain. Self-interaction of RodZ was affected by MreB actin. Deletion of this region resulted in aberrant cell shape. Our results suggest that MreB binding to the cytoplasmic domain of RodZ causes structural changes in the disordered periplasmic domain of RodZ. We also found that the disordered domain of RodZ contributes to fine-tune rod shape in E. coli.
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Affiliation(s)
- Ryosuke Ikebe
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Yuri Kuwabara
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Taiki Chikada
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Hironori Niki
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Daisuke Shiomi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
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32
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Zheng JJ, Perez AJ, Tsui HCT, Massidda O, Winkler ME. Absence of the KhpA and KhpB (JAG/EloR) RNA-binding proteins suppresses the requirement for PBP2b by overproduction of FtsA in Streptococcus pneumoniae D39. Mol Microbiol 2017; 106:793-814. [PMID: 28941257 DOI: 10.1111/mmi.13847] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2017] [Indexed: 12/11/2022]
Abstract
Suppressor mutations were isolated that obviate the requirement for essential PBP2b in peripheral elongation of peptidoglycan from the midcells of dividing Streptococcus pneumoniae D39 background cells. One suppressor was in a gene encoding a single KH-domain protein (KhpA). ΔkhpA suppresses deletions in most, but not all (mltG), genes involved in peripheral PG synthesis and in the gpsB regulatory gene. ΔkhpA mutations reduce growth rate, decrease cell size, minimally affect shape and induce expression of the WalRK cell-wall stress regulon. Reciprocal co-immunoprecipitations show that KhpA forms a complex in cells with another KH-domain protein (KhpB/JAG/EloR). ΔkhpA and ΔkhpB mutants phenocopy each other exactly, consistent with a direct interaction. RNA-immunoprecipitation showed that KhpA/KhpB bind an overlapping set of RNAs in cells. Phosphorylation of KhpB reported previously does not affect KhpB function in the D39 progenitor background. A chromosome duplication implicated FtsA overproduction in Δpbp2b suppression. We show that cellular FtsA concentration is negatively regulated by KhpA/B at the post-transcriptional level and that FtsA overproduction is necessary and sufficient for suppression of Δpbp2b. However, increased FtsA only partially accounts for the phenotypes of ΔkhpA mutants. Together, these results suggest that multimeric KhpA/B may function as a pleiotropic RNA chaperone controlling pneumococcal cell division.
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Affiliation(s)
- Jiaqi J Zheng
- Department of Biology, Indiana University Bloomington (IUB), Bloomington, IN 47405, USA
| | - Amilcar J Perez
- Department of Biology, Indiana University Bloomington (IUB), Bloomington, IN 47405, USA
| | - Ho-Ching Tiffany Tsui
- Department of Biology, Indiana University Bloomington (IUB), Bloomington, IN 47405, USA
| | - Orietta Massidda
- Dipartimento di Scienze Chirurgiche, Università di Cagliari, 09100 Cagliari, Italy
| | - Malcolm E Winkler
- Department of Biology, Indiana University Bloomington (IUB), Bloomington, IN 47405, USA
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33
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Shi H, Colavin A, Bigos M, Tropini C, Monds RD, Huang KC. Deep Phenotypic Mapping of Bacterial Cytoskeletal Mutants Reveals Physiological Robustness to Cell Size. Curr Biol 2017; 27:3419-3429.e4. [DOI: 10.1016/j.cub.2017.09.065] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 11/25/2022]
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34
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Shiomi D. Polar localization of MreB actin is inhibited by anionic phospholipids in the rod-shaped bacterium Escherichia coli. Curr Genet 2017; 63:845-848. [PMID: 28439631 DOI: 10.1007/s00294-017-0696-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 12/13/2022]
Abstract
Bacterial actin MreB is required for the maintenance of cell polarity. MreB is located underneath the cell membrane and mainly localizes at a central cylindrical part of the cell. In addition, it has recently been found that anionic phospholipids (aPLs: phosphatidylglycerol and cardiolipin) play a crucial role in excluding MreB from the cell poles. Subcellular localization of MreB is positively and negatively regulated by membrane curvature and aPLs, respectively.
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Affiliation(s)
- Daisuke Shiomi
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan.
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35
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Gardner KAJA, Osawa M, Erickson HP. Whole genome re-sequencing to identify suppressor mutations of mutant and foreign Escherichia coli FtsZ. PLoS One 2017; 12:e0176643. [PMID: 28445510 PMCID: PMC5405962 DOI: 10.1371/journal.pone.0176643] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/13/2017] [Indexed: 01/07/2023] Open
Abstract
FtsZ is an essential protein for bacterial cell division, where it forms the cytoskeletal scaffold and may generate the constriction force. We have found previously that some mutant and foreign FtsZ that do not complement an ftsZ null can function for cell division in E. coli upon acquisition of a suppressor mutation somewhere in the genome. We have now identified, via whole genome re-sequencing, single nucleotide polymorphisms in 11 different suppressor strains. Most of the mutations are in genes of various metabolic pathways, which may modulate cell division indirectly. Mutations in three genes, ispA, accD and nlpI, may be more directly involved in cell division. In addition to the genomic suppressor mutations, we identified intragenic suppressors of three FtsZ point mutants (R174A, E250K and L272V).
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Affiliation(s)
- Kiani A. J. Arkus Gardner
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Masaki Osawa
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Harold P. Erickson
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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36
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Kawazura T, Matsumoto K, Kojima K, Kato F, Kanai T, Niki H, Shiomi D. Exclusion of assembled MreB by anionic phospholipids at cell poles confers cell polarity for bidirectional growth. Mol Microbiol 2017; 104:472-486. [PMID: 28164388 DOI: 10.1111/mmi.13639] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2017] [Indexed: 12/21/2022]
Abstract
Cell polarity determines the direction of cell growth in bacteria. MreB actin spatially regulates peptidoglycan synthesis to enable cells to elongate bidirectionally. MreB densely localizes in the cylindrical part of the rod cell and not in polar regions in Escherichia coli. When treated with A22, which inhibits MreB polymerization, rod-shaped cells became round and MreB was diffusely distributed throughout the cytoplasmic membrane. A22 removal resulted in restoration of the rod shape. Initially, diffuse MreB started to re-assemble, and MreB-free zones were subsequently observed in the cytoplasmic membrane. These MreB-free zones finally became cell poles, allowing the cells to elongate bidirectionally. When MreB was artificially located at the cell poles, an additional pole was created, indicating that artificial localization of MreB at the cell pole induced local peptidoglycan synthesis. It was found that the anionic phospholipids (aPLs), phosphatidylglycerol and cardiolipin, which were enriched in cell poles preferentially interact with monomeric MreB compared with assembled MreB in vitro. MreB tended to localize to cell poles in cells lacking both aPLs, resulting in production of Y-shaped cells. Their findings indicated that aPLs exclude assembled MreB from cell poles to establish cell polarity, thereby allowing cells to elongate in a particular direction.
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Affiliation(s)
- Takuma Kawazura
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Kanon Matsumoto
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Koki Kojima
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Fumiya Kato
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Tomomi Kanai
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Hironori Niki
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, Sokendai, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Daisuke Shiomi
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
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37
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Winkler JD, Halweg-Edwards AL, Erickson KE, Choudhury A, Pines G, Gill RT. The Resistome: A Comprehensive Database of Escherichia coli Resistance Phenotypes. ACS Synth Biol 2016; 5:1566-1577. [PMID: 27438180 DOI: 10.1021/acssynbio.6b00150] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The microbial ability to resist stressful environmental conditions and chemical inhibitors is of great industrial and medical interest. Much of the data related to mutation-based stress resistance, however, is scattered through the academic literature, making it difficult to apply systematic analyses to this wealth of information. To address this issue, we introduce the Resistome database: a literature-curated collection of Escherichia coli genotypes-phenotypes containing over 5,000 mutants that resist hundreds of compounds and environmental conditions. We use the Resistome to understand our current state of knowledge regarding resistance and to detect potential synergy or antagonism between resistance phenotypes. Our data set represents one of the most comprehensive collections of genomic data related to resistance currently available. Future development will focus on the construction of a combined genomic-transcriptomic-proteomic framework for understanding E. coli's resistance biology. The Resistome can be downloaded at https://bitbucket.org/jdwinkler/resistome_release/overview .
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Affiliation(s)
- James D. Winkler
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Andrea L. Halweg-Edwards
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Keesha E. Erickson
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Alaksh Choudhury
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Gur Pines
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Ryan T. Gill
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
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38
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Gouran H, Gillespie H, Nascimento R, Chakraborty S, Zaini PA, Jacobson A, Phinney BS, Dolan D, Durbin-Johnson BP, Antonova ES, Lindow SE, Mellema MS, Goulart LR, Dandekar AM. The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa. Sci Rep 2016; 6:31098. [PMID: 27492542 PMCID: PMC4974619 DOI: 10.1038/srep31098] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/13/2016] [Indexed: 11/09/2022] Open
Abstract
Pierce's disease (PD) is a deadly disease of grapevines caused by the Gram-negative bacterium Xylella fastidiosa. Though disease symptoms were formerly attributed to bacteria blocking the plant xylem, this hypothesis is at best overly simplistic. Recently, we used a proteomic approach to characterize the secretome of X. fastidiosa, both in vitro and in planta, and identified LesA as one of the pathogenicity factors of X. fastidiosa in grapevines that leads to leaf scorching and chlorosis. Herein, we characterize another such factor encoded by PD0956, designated as an antivirulence secreted protease "PrtA" that displays a central role in controlling in vitro cell proliferation, length, motility, biofilm formation, and in planta virulence. The mutant in X. fastidiosa exhibited reduced cell length, hypermotility (and subsequent lack of biofilm formation) and hypervirulence in grapevines. These findings are supported by transcriptomic and proteomic analyses with corresponding plant infection data. Of particular interest, is the hypervirulent response in grapevines observed when X. fastidiosa is disrupted for production of PrtA, and that PD-model tobacco plants transformed to express PrtA exhibited decreased symptoms after infection by X. fastidiosa.
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Affiliation(s)
- Hossein Gouran
- Plant Sciences Department, University of California, Davis, CA, USA
| | - Hyrum Gillespie
- Plant Sciences Department, University of California, Davis, CA, USA
| | - Rafael Nascimento
- Plant Sciences Department, University of California, Davis, CA, USA
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Brazil
| | | | - Paulo A. Zaini
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Brazil
| | - Aaron Jacobson
- Plant Sciences Department, University of California, Davis, CA, USA
| | - Brett S. Phinney
- Proteomics Core, Genome Center, University of California, Davis, USA
| | - David Dolan
- Plant Sciences Department, University of California, Davis, CA, USA
| | | | - Elena S. Antonova
- Plant and Microbial Biology Department, University of Berkeley, Berkeley, CA, USA
| | - Steven E. Lindow
- Plant and Microbial Biology Department, University of Berkeley, Berkeley, CA, USA
| | - Matthew S. Mellema
- Surgical and Radiological Sciences, Vet Med, University of California, Davis, CA, USA
| | - Luiz R. Goulart
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Brazil
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
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39
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YodL and YisK Possess Shape-Modifying Activities That Are Suppressed by Mutations in Bacillus subtilis mreB and mbl. J Bacteriol 2016; 198:2074-88. [PMID: 27215790 DOI: 10.1128/jb.00183-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/18/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Many bacteria utilize actin-like proteins to direct peptidoglycan (PG) synthesis. MreB and MreB-like proteins are thought to act as scaffolds, guiding the localization and activity of key PG-synthesizing proteins during cell elongation. Despite their critical role in viability and cell shape maintenance, very little is known about how the activity of MreB family proteins is regulated. Using a Bacillus subtilis misexpression screen, we identified two genes, yodL and yisK, that when misexpressed lead to loss of cell width control and cell lysis. Expression analysis suggested that yodL and yisK are previously uncharacterized Spo0A-regulated genes, and consistent with these observations, a ΔyodL ΔyisK mutant exhibited reduced sporulation efficiency. Suppressors resistant to YodL's killing activity occurred primarily in mreB mutants and resulted in amino acid substitutions at the interface between MreB and the highly conserved morphogenic protein RodZ, whereas suppressors resistant to YisK occurred primarily in mbl mutants and mapped to Mbl's predicted ATP-binding pocket. YodL's shape-altering activity appears to require MreB, as a ΔmreB mutant was resistant to the effects of YodL but not YisK. Similarly, YisK appears to require Mbl, as a Δmbl mutant was resistant to the cell-widening effects of YisK but not of YodL. Collectively, our results suggest that YodL and YisK likely modulate MreB and Mbl activity, possibly during the early stages of sporulation. IMPORTANCE The peptidoglycan (PG) component of the cell envelope confers structural rigidity to bacteria and protects them from osmotic pressure. MreB and MreB-like proteins are thought to act as scaffolds for PG synthesis and are essential in bacteria exhibiting nonpolar growth. Despite the critical role of MreB-like proteins, we lack mechanistic insight into how their activities are regulated. Here, we describe the discovery of two B. subtilis proteins, YodL and YisK, which modulate MreB and Mbl activities. Our data suggest that YodL specifically targets MreB, whereas YisK targets Mbl. The apparent specificities with which YodL and YisK are able to differentially target MreB and Mbl make them potentially powerful tools for probing the mechanics of cytoskeletal function in bacteria.
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Jiang XR, Chen GQ. Morphology engineering of bacteria for bio-production. Biotechnol Adv 2016; 34:435-440. [DOI: 10.1016/j.biotechadv.2015.12.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/08/2015] [Accepted: 12/16/2015] [Indexed: 01/19/2023]
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Abstract
With the realization that bacteria achieve exquisite levels of spatiotemporal organization has come the challenge of discovering the underlying mechanisms. In this review, we describe three classes of such mechanisms, each of which has physical origins: the use of landmarks, the creation of higher-order structures that enable geometric sensing, and the emergence of length scales from systems of chemical reactions coupled to diffusion. We then examine the diversity of geometric cues that exist even in cells with relatively simple geometries, and end by discussing both new technologies that could drive further discovery and the implications of our current knowledge for the behavior, fitness, and evolution of bacteria. The organizational strategies described here are employed in a wide variety of systems and in species across all kingdoms of life; in many ways they provide a general blueprint for organizing the building blocks of life.
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Affiliation(s)
- Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544;
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Laddomada F, Miyachiro MM, Dessen A. Structural Insights into Protein-Protein Interactions Involved in Bacterial Cell Wall Biogenesis. Antibiotics (Basel) 2016; 5:antibiotics5020014. [PMID: 27136593 PMCID: PMC4929429 DOI: 10.3390/antibiotics5020014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 03/15/2016] [Accepted: 04/09/2016] [Indexed: 12/30/2022] Open
Abstract
The bacterial cell wall is essential for survival, and proteins that participate in its biosynthesis have been the targets of antibiotic development efforts for decades. The biosynthesis of its main component, the peptidoglycan, involves the coordinated action of proteins that are involved in multi-member complexes which are essential for cell division (the “divisome”) and/or cell wall elongation (the “elongasome”), in the case of rod-shaped cells. Our knowledge regarding these interactions has greatly benefitted from the visualization of different aspects of the bacterial cell wall and its cytoskeleton by cryoelectron microscopy and tomography, as well as genetic and biochemical screens that have complemented information from high resolution crystal structures of protein complexes involved in divisome or elongasome formation. This review summarizes structural and functional aspects of protein complexes involved in the cytoplasmic and membrane-related steps of peptidoglycan biosynthesis, with a particular focus on protein-protein interactions whereby disruption could lead to the development of novel antibacterial strategies.
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Affiliation(s)
- Federica Laddomada
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Grenoble F-38044, France.
- Centre National de la Recherche Scientifique (CNRS), IBS, Grenoble F-38044, France.
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), IBS, Grenoble F-38044, France.
| | - Mayara M Miyachiro
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo 13083-100, Brazil.
| | - Andréa Dessen
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, Grenoble F-38044, France.
- Centre National de la Recherche Scientifique (CNRS), IBS, Grenoble F-38044, France.
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), IBS, Grenoble F-38044, France.
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo 13083-100, Brazil.
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RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis. Proc Natl Acad Sci U S A 2015; 112:12510-5. [PMID: 26396257 DOI: 10.1073/pnas.1509610112] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The rod shape of most bacteria requires the actin homolog, MreB. Whereas MreB was initially thought to statically define rod shape, recent studies found that MreB dynamically rotates around the cell circumference dependent on cell wall synthesis. However, the mechanism by which cytoplasmic MreB is linked to extracytoplasmic cell wall synthesis and the function of this linkage for morphogenesis has remained unclear. Here we demonstrate that the transmembrane protein RodZ mediates MreB rotation by directly or indirectly coupling MreB to cell wall synthesis enzymes. Furthermore, we map the RodZ domains that link MreB to cell wall synthesis and identify mreB mutants that suppress the shape defect of ΔrodZ without restoring rotation, uncoupling rotation from rod-like growth. Surprisingly, MreB rotation is dispensable for rod-like shape determination under standard laboratory conditions but is required for the robustness of rod shape and growth under conditions of cell wall stress.
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van der Ploeg R, Goudelis ST, den Blaauwen T. Validation of FRET Assay for the Screening of Growth Inhibitors of Escherichia coli Reveals Elongasome Assembly Dynamics. Int J Mol Sci 2015; 16:17637-54. [PMID: 26263980 PMCID: PMC4581212 DOI: 10.3390/ijms160817637] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 07/21/2015] [Accepted: 07/24/2015] [Indexed: 11/16/2022] Open
Abstract
The increase in antibiotic resistant bacteria demands the development of new antibiotics against preferably new targets. The common approach is to test compounds for their ability to kill bacteria or to design molecules that inhibit essential protein activities in vitro. In the first case, the mode of action of the drug is unknown and in the second case, it is not known whether the compound will pass the impermeable barrier of the bacterial envelope. We developed an assay that detects the target of a compound, as well as its ability to pass the membrane(s) simultaneously. The Escherichia coli cytoskeletal protein MreB recruits protein complexes (elongasomes) that are essential for cell envelope growth. An in cell Förster Resonance Energy Transfer (FRET) assay was developed to detect the interaction between MreB molecules and between MreB and the elongasome proteins RodZ, RodA and PBP2. Inhibition of the polymerization of MreB by S-(3,4-dichlorobenzyl) isothiourea (A22) or of the activity of PBP2 by mecilinam resulted in loss or reduction of all measured interactions. This suggests that the interactions between the elongasome proteins are governed by a combination of weak affinities and substrate availability. This validated in cell FRET assay can be used to screen for cell envelope growth inhibitors.
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Affiliation(s)
- René van der Ploeg
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherland.
| | - Spyridon Theodoros Goudelis
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherland.
| | - Tanneke den Blaauwen
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherland.
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Shiomi D. [Regulation of determination of bacterial shape]. Nihon Saikingaku Zasshi 2014; 69:557-64. [PMID: 25447981 DOI: 10.3412/jsb.69.557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacteria show various cell shape such as round, rod, helical, and so on. However, each bacterium has its own shape and their length and width are kept in a narrow range in a population. Abnormal cell shape often results in death of the cells. Therefore, it is important to maintain their shape. Rod-shaped bacterium Escherichia coli needs to regulate cell polarity, length and width in order to form rod shape. Bacterial shape is genetically regulated. Especially, MreB, a bacterial actin, and its interacting proteins are involved in the regulation. We have identified rodZ as a novel cell shape determinant and have been analyzing RodZ protein in the past few years. The rodZ mutant is round. We isolated suppressor mutants of the rodZ mutant. The shape of the suppressors was rod shape. By analyzing the rodZ mutant and the suppressors, we concluded that RodZ helps assembly of MreB filaments. MreB plays roles in regulation of cell polarity, length, and width, whereas RodZ is involved in regulation of length and width. In this review, I summarize our research and research from other groups on bacterial cell shape.
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Affiliation(s)
- Daisuke Shiomi
- Department of Life Science, College of Science, Rikkyo University
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Evolved osmotolerant Escherichia coli mutants frequently exhibit defective N-acetylglucosamine catabolism and point mutations in cell shape-regulating protein MreB. Appl Environ Microbiol 2014; 80:3729-40. [PMID: 24727267 DOI: 10.1128/aem.00499-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Biocatalyst robustness toward stresses imposed during fermentation is important for efficient bio-based production. Osmotic stress, imposed by high osmolyte concentrations or dense populations, can significantly impact growth and productivity. In order to better understand the osmotic stress tolerance phenotype, we evolved sexual (capable of in situ DNA exchange) and asexual Escherichia coli strains under sodium chloride (NaCl) stress. All isolates had significantly improved growth under selection and could grow in up to 0.80 M (47 g/liter) NaCl, a concentration that completely inhibits the growth of the unevolved parental strains. Whole genome resequencing revealed frequent mutations in genes controlling N-acetylglucosamine catabolism (nagC, nagA), cell shape (mrdA, mreB), osmoprotectant uptake (proV), and motility (fimA). Possible epistatic interactions between nagC, nagA, fimA, and proV deletions were also detected when reconstructed as defined mutations. Biofilm formation under osmotic stress was found to be decreased in most mutant isolates, coupled with perturbations in indole secretion. Transcriptional analysis also revealed significant changes in ompACGL porin expression and increased transcription of sulfonate uptake systems in the evolved mutants. These findings expand our current knowledge of the osmotic stress phenotype and will be useful for the rational engineering of osmotic tolerance into industrial strains in the future.
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Do the divisome and elongasome share a common evolutionary past? Curr Opin Microbiol 2013; 16:745-51. [DOI: 10.1016/j.mib.2013.09.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/20/2013] [Accepted: 09/06/2013] [Indexed: 01/05/2023]
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Cava F, Kuru E, Brun YV, de Pedro MA. Modes of cell wall growth differentiation in rod-shaped bacteria. Curr Opin Microbiol 2013; 16:731-7. [PMID: 24094807 DOI: 10.1016/j.mib.2013.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/21/2013] [Accepted: 09/06/2013] [Indexed: 10/26/2022]
Abstract
A bacterial cell takes on the challenge to preserve and reproduce its shape at every generation against a substantial internal pressure by surrounding itself with a mechanical support, a peptidoglycan cell wall. The enlargement of the cell wall via net incorporation of precursors into the pre-existing wall conditions bacterial growth and morphology. However, generation, reproduction and/or modification of a specific shape requires that the incorporation takes place at precise locations for a defined time period. Much has been learnt in the past few years about the biochemistry of the peptidoglycan synthesis process, but topological approaches to the understanding of shape generation have been hindered by a lack of appropriate techniques. Recent technological advances are paving the way for substantial progress in understanding the mechanisms of bacterial morphogenesis. Here we review the latest developments, focusing on the impact of new techniques on the precise mapping of cell wall growth sites.
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Affiliation(s)
- Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.
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Shiomi D, Niki H. A mutation in the promoter region of zipA, a component of the divisome, suppresses the shape defect of RodZ-deficient cells. Microbiologyopen 2013; 2:798-810. [PMID: 23922320 PMCID: PMC3831641 DOI: 10.1002/mbo3.116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/14/2013] [Accepted: 06/24/2013] [Indexed: 11/07/2022] Open
Abstract
RodZ is important for maintaining the rod shape of Escherichia coli. Loss of RodZ causes conversion of the rod shape to a round shape and a growth rate slower than that of wild-type cells. Suppressor mutations that simultaneously restore both the growth rates and the rod shape were isolated. Most of the suppressor mutations are found in mreB, mrdA, or mrdB. One of the mutations was in the promoter region of zipA, which encodes a crucial component of the cell division machinery. In this study, we investigated the mechanism of the suppression by this mutation. ZipA was slightly but significantly increased in the suppressor cells and led to a delay in cell division. While round-shaped mreB and mrdA mutants lose cell bipolarity, we found that round-shaped rodZ mutants retained cell bipolarity. Therefore, we concluded that a delay in the completion of septation provides extra time to elongate the cell laterally so that the zipA suppressor mutant is able to recover its ovoid or rod shape. The suppression by zipA demonstrates that the regulation of timing of septation potentially contributes to the conversion of morphology in bacterial cells.
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Affiliation(s)
- Daisuke Shiomi
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Sokendai, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
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