1
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Wilson SA, Tank RKJ, Hobbs JK, Foster SJ, Garner EC. An exhaustive multiple knockout approach to understanding cell wall hydrolase function in Bacillus subtilis. mBio 2023; 14:e0176023. [PMID: 37768080 PMCID: PMC10653849 DOI: 10.1128/mbio.01760-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/03/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE In order to grow, bacterial cells must both create and break down their cell wall. The enzymes that are responsible for these processes are the target of some of our best antibiotics. Our understanding of the proteins that break down the wall- cell wall hydrolases-has been limited by redundancy among the large number of hydrolases many bacteria contain. To solve this problem, we identified 42 cell wall hydrolases in Bacillus subtilis and created a strain lacking 40 of them. We show that cells can survive using only a single cell wall hydrolase; this means that to understand the growth of B. subtilis in standard laboratory conditions, it is only necessary to study a very limited number of proteins, simplifying the problem substantially. We additionally show that the ∆40 strain is a research tool to characterize hydrolases, using it to identify three "helper" hydrolases that act in certain stress conditions.
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Affiliation(s)
- Sean A. Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Raveen K. J. Tank
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Jamie K. Hobbs
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Simon J. Foster
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ethan C. Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA
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2
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Christie G, Setlow P. Bacillus spore germination: Knowns, unknowns and what we need to learn. Cell Signal 2020; 74:109729. [PMID: 32721540 DOI: 10.1016/j.cellsig.2020.109729] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 01/06/2023]
Abstract
How might a microbial cell that is entirely metabolically dormant - and which has the ability to remain so for extended periods of time - irreversibly commit itself to resuming vegetative growth within seconds of being exposed to certain amino acids or sugars? That this process takes place in the absence of any detectable ATP or de novo protein synthesis, and relies upon a pre-formed apparatus that is immobilised, respectively, in a semi-crystalline membrane or multi-layered proteinaceous coat, only exacerbates the challenge facing spores of Bacillales species when stimulated to germinate. Whereas the process by which spores are formed in response to nutrient starvation - sporulation - involves the orchestrated interplay between hundreds of distinct proteins, the process by which spores return to life - germination - is a much simpler affair, requiring a handful of receptor and channel proteins complemented with specialized peptidoglycan lysins. Despite this relative simplicity, and research effort spanning many decades, comprehensive understanding of key molecular and biochemical details and, in particular signal transduction mechanisms associated with spore germination, has remained elusive. In this review we provide an up to date overview of the field while identifying what we consider to be the key gaps in knowledge associated with germination of Bacillales spores, suggesting also technical approaches that may provide fresh insight to this unique biological process.
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Affiliation(s)
- Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 OAS, United Kingdom.
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA.
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3
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Aspholm ME, Kollerud KK, Høgberg Hansen HC, Granum PE, Christie G, Lindbäck T. Biochemical and mutational analysis of spore cortex-lytic enzymes in the food spoiler Bacillus licheniformis. Food Microbiol 2019; 84:103259. [PMID: 31421778 DOI: 10.1016/j.fm.2019.103259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/01/2019] [Accepted: 07/03/2019] [Indexed: 12/11/2022]
Abstract
Bacillus licheniformis is frequently associated with food spoilage due to its ability to form highly resistant endospores. The present study reveals that B. licheniformis spore peptidoglycan shares a similar structure to spores of other species of Bacillus. Two enzymatic activities associated with depolymerisation of the cortical peptidoglycan, which represents a crucial step in spore germination, were detected by muropeptide analysis. These include lytic transglycosylase and N-acetylglucosaminidase activity, with non-lytic epimerase activity also being detected. The role of various putative cortex-lytic enzymes that account for the aforementioned activity was investigated by mutational analysis. These analyses indicate that SleB is the major lysin involved in cortex depolymerisation in B. licheniformis spores, with CwlJ and SleL having lesser roles. Collectively, the results of this work indicate that B. licheniformis spores employ a similar approach for cortical depolymerisation during germination as spores of other Bacillus species.
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Affiliation(s)
- Marina E Aspholm
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Pb 369 Sentrum, 0102, Oslo, Norway
| | - Kristian K Kollerud
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Pb 369 Sentrum, 0102, Oslo, Norway
| | - Helge C Høgberg Hansen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Pb 369 Sentrum, 0102, Oslo, Norway
| | - Per Einar Granum
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Pb 369 Sentrum, 0102, Oslo, Norway
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Toril Lindbäck
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Pb 369 Sentrum, 0102, Oslo, Norway.
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Riyami BA, Ghosh A, Rees EJ, Christie G. Novel cortex lytic enzymes in Bacillus megaterium QM B1551 spores. FEMS Microbiol Lett 2019; 366:5527933. [DOI: 10.1093/femsle/fnz146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/02/2019] [Indexed: 11/15/2022] Open
Abstract
ABSTRACTPresent models for spore germination in Bacillus species include a requirement for either the SleB or CwlJ cortex lytic enzymes to efficiently depolymerise the spore cortex. Previous work has demonstrated that B. megaterium spores may differ to other species in this regard, since sleB cwlJ null mutant spores complemented with the gene in trans for the non-peptidoglycan lysin YpeB can efficiently degrade the cortex. Here, we identify two novel cortex lytic enzymes, encoded at the BMQ_2391 and BMQ_3234 loci, which are essential for cortex hydrolysis in the absence of SleB and CwlJ. Ellipsoid localisation microscopy places the BMQ_3234 protein within the inner-spore coat, a region of the spore that is populated by other cortex lytic enzymes. The findings reinforce the idea that there is a degree of variation in mechanisms of cortex hydrolysis across the Bacillales, raising potential implications for environmental decontamination strategies based upon targeted inactivation of components of the spore germination apparatus.
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Affiliation(s)
- Bahja Al Riyami
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Abhinaba Ghosh
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Eric J Rees
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
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Stelder SK, Benito de Moya C, Hoefsloot HCJ, de Koning LJ, Brul S, de Koster CG. Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach. J Proteome Res 2018; 17:903-917. [PMID: 29260567 PMCID: PMC5799878 DOI: 10.1021/acs.jproteome.7b00732] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Spores of Bacillus cereus pose a threat to food
safety due to their high resistance to the heat or acid treatments
commonly used to make food microbiologically safe. Spores may survive
these treatments and later resume growth either on foodstuffs or,
after ingestion, upon entering the gut they are capable of producing
toxins, which cause either vomiting or diarrhea. The outer layers
of the spore, the spore coat and exosporium, consist primarily of
proteins that may serve as potential biomarkers for detection. The
major morphogenetic protein CotE is important for correct assembly
and attachment of the outermost layer, the exosporium, and by extension
retention of many proteins. However, characterization of the proteins
affected by deletion of CotE has been limited to electrophoretic patterns.
Here we report the effect of CotE deletion on the insoluble fraction
of the spore proteome through liquid chromatography–Fourier
transform tandem mass spectrometry (LC–FTMS/MS) analysis. A total of 560 proteins have been identified in both mutant
and wild-type spore coat isolates. A further 163 proteins were identified
exclusively in wild-type spore isolates indicating that they are dependent
on CotE for their association with the spore. Several of these are
newly confirmed as associated with the exosporium, namely BC_2569
(BclF), BC_3345, BC_2427, BC_2878, BC_0666, BC_2984, BC_3481, and
BC_2570. A total of 153 proteins were only identified in ΔCotE
spore isolates. This was observed for proteins that are known or likely
to be interacting with or are encased by CotE. Crucial spore proteins
were quantified using a QconCAT reference standard, the first time
this was used in a biochemically heterogeneous system. This allowed
us to determine the absolute abundance of 21 proteins, which spanned
across three orders of magnitude and together covered 5.66% ±
0.51 of the total spore weight. Applying the QconCAT methodology to
the ΔCotE mutant allowed us to quantify 4.13% ± 0.14 of
the spore total weight and revealed a reduction in abundance for most
known exosporium associated proteins upon CotE deletion. In contrast,
several proteins, either known or likely to be interacting with or
encased by CotE (i.e., GerQ), were more abundant. The results obtained
provide deeper insight into the layered spore structure such as which
proteins are exposed on the outside of the spore. This information
is important for developing detection methods for targeting spores
in a food safety setting. Furthermore, protein stoichiometry and determination
of the abundance of germination mediating enzymes provides useful
information for germination and outgrowth model development.
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Affiliation(s)
- Sacha K Stelder
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Celia Benito de Moya
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Huub C J Hoefsloot
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Leo J de Koning
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Stanley Brul
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Chris G de Koster
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
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Liu T, Zhu W, Wang J, Zhou Y, Duan Y, Qu M, Yang Q. The deduced role of a chitinase containing two nonsynergistic catalytic domains. Acta Crystallogr D Struct Biol 2018; 74:30-40. [PMID: 29372897 PMCID: PMC5786006 DOI: 10.1107/s2059798317018289] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/21/2017] [Indexed: 01/27/2023] Open
Abstract
The glycoside hydrolase family 18 chitinases degrade or alter chitin. Multiple catalytic domains in a glycoside hydrolase family 18 chitinase function synergistically during chitin degradation. Here, an insect group III chitinase from the agricultural pest Ostrinia furnacalis (OfChtIII) is revealed to be an arthropod-conserved chitinase that contains two nonsynergistic GH18 domains according to its catalytic properties. Both GH18 domains are active towards single-chained chitin substrates, but are inactive towards insoluble chitin substrates. The crystal structures of each unbound GH18 domain, as well as of GH18 domains complexed with hexa-N-acetyl-chitohexaose or penta-N-acetyl-chitopentaose, suggest that the two GH18 domains possess endo-specific activities. Physiological data indicated that the developmental stage-dependent gene-expression pattern of OfChtIII was the same as that of the chitin synthase OfChsA but significantly different from that of the chitinase OfChtI, which is indispensable for cuticular chitin degradation. Additionally, immunological staining indicated that OfChtIII was co-localized with OfChsA. Thus, OfChtIII is most likely to be involved in the chitin-synthesis pathway.
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Affiliation(s)
- Tian Liu
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Weixing Zhu
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Jing Wang
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Yong Zhou
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Yanwei Duan
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Mingbo Qu
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Qing Yang
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, People’s Republic of China
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Abstract
Dormant Bacillales and Clostridiales spores begin to grow when small molecules (germinants) trigger germination, potentially leading to food spoilage or disease. Germination-specific proteins sense germinants, transport small molecules, and hydrolyze specific bonds in cortex peptidoglycan and specific proteins. Major events in germination include (a) germinant sensing; (b) commitment to germinate; (c) release of spores' depot of dipicolinic acid (DPA); (d) hydrolysis of spores' peptidoglycan cortex; and (e) spore core swelling and water uptake, cell wall peptidoglycan remodeling, and restoration of core protein and inner spore membrane lipid mobility. Germination is similar between Bacillales and Clostridiales, but some species differ in how germinants are sensed and how cortex hydrolysis and DPA release are triggered. Despite detailed knowledge of the proteins and signal transduction pathways involved in germination, precisely what some germination proteins do and how they do it remain unclear.
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Affiliation(s)
- Peter Setlow
- Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut 06030-3305;
| | - Shiwei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Yong-Qing Li
- Department of Physics, East Carolina University, Greenville, North Carolina 27858-4353;
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8
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Abstract
Spores of Clostridiales and Bacillales are encased in a complex series of concentric shells that provide protection, facilitate germination, and mediate interactions with the environment. Analysis of diverse spore-forming species by thin-section transmission electron microscopy reveals that the number and morphology of these encasing shells vary greatly. In some species, they appear to be composed of a small number of discrete layers. In other species, they can comprise multiple, morphologically complex layers. In addition, spore surfaces can possess elaborate appendages. For all their variability, there is a consistent architecture to the layers encasing the spore. A hallmark of all Clostridiales and Bacillales spores is the cortex, a layer made of peptidoglycan. In close association with the cortex, all species examined possess, at a minimum, a series of proteinaceous layers, called the coat. In some species, including Bacillus subtilis, only the coat is present. In other species, including Bacillus anthracis, an additional layer, called the exosporium, surrounds the coat. Our goals here are to review the present understanding of the structure, composition, assembly, and functions of the coat, primarily in the model organism B. subtilis, but also in the small but growing number of other spore-forming species where new data are showing that there is much to be learned beyond the relatively well-developed basis of knowledge in B. subtilis. To help summarize this large field and define future directions for research, we will focus on key findings in recent years.
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Al-Riyami B, Üstok FI, Stott K, Chirgadze DY, Christie G. The crystal structure of Clostridium perfringens SleM, a muramidase involved in cortical hydrolysis during spore germination. Proteins 2016; 84:1681-1689. [PMID: 27488615 DOI: 10.1002/prot.25112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/05/2016] [Accepted: 07/25/2016] [Indexed: 01/10/2023]
Abstract
Clostridium perfringens spores employ two peptidoglycan lysins to degrade the spore cortex during germination. SleC initiates cortex hydrolysis to generate cortical fragments that are degraded further by the muramidase SleM. Here, we present the crystal structure of the C. perfringens S40 SleM protein at 1.8 Å. SleM comprises an N-terminal catalytic domain that adopts an irregular α/β-barrel fold that is common to GH25 family lysozymes, plus a C-terminal fibronectin type III domain. The latter is involved in forming the SleM dimer that is evident in both the crystal structure and in solution. A truncated form of SleM that lacks the FnIII domain shows reduced activity against spore sacculi indicating that this domain may have a role in facilitating the position of substrate with respect to the enzyme's active site. Proteins 2016; 84:1681-1689. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Bahja Al-Riyami
- Department of Chemical Engineering and Biotechnology, Institute of Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Fatma Işık Üstok
- Department of Haematology, Division of Structural Medicine and Thrombosis Research Unit, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Dimitri Y Chirgadze
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, Institute of Biotechnology, University of Cambridge, Cambridge, United Kingdom.
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