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Zhang X, Chen Y, Yan T, Wang H, Zhang R, Xu Y, Hou Y, Peng Q, Song F. Cell death dependent on holins LrgAB repressed by a novel ArsR family regulator CdsR. Cell Death Discov 2024; 10:173. [PMID: 38605001 PMCID: PMC11009283 DOI: 10.1038/s41420-024-01942-3] [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: 12/28/2023] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024] Open
Abstract
The cell death and survival paradox in various biological processes requires clarification. While spore development causes maternal cell death in Bacillus species, the involvement of other cell death pathways in sporulation remains unknown. Here, we identified a novel ArsR family transcriptional regulator, CdsR, and found that the deletion of its encoding gene cdsR causes cell lysis and inhibits sporulation. To our knowledge, this is the first report of an ArsR family transcriptional regulator governing cell death. We found that CdsR directly repressed lrgAB expression. Furthermore, lrgAB overexpression resulted in cell lysis without sporulation, akin to the cdsR mutant, suggesting that LrgAB, a holin-like protein, induces cell death in Bacillus spp. The lrgAB mutation increases abnormal cell numbers during spore development. In conclusion, we propose that a novel repressor is vital for inhibiting LrgAB-dependent cell lysis.
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Affiliation(s)
- Xin Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Tinglu Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hengjie Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruibin Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanrong Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yujia Hou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Fuping Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
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Carrizo AE, Del Valle Loto F, Baigorí MD, Pera LM. Bacillus thuringiensis-Based Bioproduct: Characterization and Performance Against Spodoptera frugiperda Strains in Maize Under Different Environmental Temperatures. NEOTROPICAL ENTOMOLOGY 2023; 52:283-291. [PMID: 35731370 DOI: 10.1007/s13744-022-00973-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) is an important pest in several regions being the use of Bacillus thuringiensis-based bioproducts an alternative for its control. Firstly, 3 L of an aqueous bioproduct suspension was produced and characterized. Its 50% lethal concentration against molecularly identified corn and rice S. frugiperda strains using an artificial diet were 77.01% (95% CL, 68.16-90.47) and 2.22% (95% CL, 0.01-6.68), respectively. The next objective of this work was to evaluate the performance of this bioproduct in maize against S. frugiperda strains under different simulated agrological regions mimicking their corresponding periodic day/night temperatures. Thus, the impact of environmental temperature on the bioproduct efficacy (E) was studied. It was observed that a warmer scenario (35 °C day/30 °C night) could favor the tolerance of corn S. frugiperda strain to the bioproduct (E = 56.36 ± 0.61%) maintaining a high efficacy (92.44 ± 6.55%) when it was tested against rice S. frugiperda strain. Conversely, under temperate conditions, efficacy values ranged from 84 to 95% for both S. frugiperda strains. On the other hand, based on a foliar feeding damage analysis, our bioproduct displayed a significant foliar protection in maize plants infested with either corn or rice S. frugiperda strains.
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Affiliation(s)
- Alfonso Emanuel Carrizo
- Morphogenesis and Fermentation Lab, PROIMI-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Flavia Del Valle Loto
- Morphogenesis and Fermentation Lab, PROIMI-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Mario Domingo Baigorí
- Morphogenesis and Fermentation Lab, PROIMI-CONICET, San Miguel de Tucumán, Tucumán, Argentina
- Facultad de Bioquímica, Química y Farmacia, Cátedra de Microbiología Superior, Univ Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Licia María Pera
- Morphogenesis and Fermentation Lab, PROIMI-CONICET, San Miguel de Tucumán, Tucumán, Argentina.
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In silico insight of cell-death-related proteins in photosynthetic cyanobacteria. Arch Microbiol 2022; 204:511. [PMID: 35864385 DOI: 10.1007/s00203-022-03130-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/02/2022]
Abstract
Cyanobacteria are a large group of ubiquitously found photosynthetic prokaryotes that are constantly exposed to different kinds of stressors of varying intensities and seem to overcome these in a precise and regulated manner. However, a high dose and duration of given stress induce cell death in a few select cyanobacteria, mainly to protect other cells (altruism). Despite the recent findings for the presence of biochemical and molecular hallmarks of cell death in cyanobacteria, it is yet a sketchily understood phenomenon. Regulation of metacaspase-like genes during Programmed Cell Death suggests it to be a genetically controlled mechanism like other eukaryotes. In addition to providing a comprehensive understanding of the current status of cell death in cyanobacteria, this review has used in silico analyses to directly compare the existence of some important molecular players operating in the intrinsic and extrinsic apoptotic pathways. Phylogenetic trees for all sequences indicate a cluster with a common ancestry and also a divergence from sequences of eukaryotic origin. To the best of our knowledge, such a comparison (except for orthocaspases) has not been attempted earlier and hopes to encourage workers in the field to investigate this altruistic phenomenon in detail.
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A security check that monitors cell morphogenesis. Trends Microbiol 2022; 30:405-407. [PMID: 35346552 DOI: 10.1016/j.tim.2022.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/23/2022]
Abstract
Bacterial endospore formation depends on a series of checkpoints to ensure the fidelity of this critical developmental process. Delerue et al. have uncovered a novel checkpoint in Bacillus subtilis that senses defects in the assembly of static polymers in one compartment and arrests the assembly of peptidoglycan in another compartment.
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Delerue T, Anantharaman V, Gilmore MC, Popham DL, Cava F, Aravind L, Ramamurthi KS. Bacterial developmental checkpoint that directly monitors cell surface morphogenesis. Dev Cell 2022; 57:344-360.e6. [PMID: 35065768 PMCID: PMC8991396 DOI: 10.1016/j.devcel.2021.12.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 11/15/2021] [Accepted: 12/20/2021] [Indexed: 01/05/2023]
Abstract
Bacillus subtilis spores are encased in two concentric shells: an outer proteinaceous "coat" and an inner peptidoglycan "cortex," separated by a membrane. Cortex assembly depends on coat assembly initiation, but how cells achieve this coordination across the membrane is unclear. Here, we report that the protein SpoVID monitors the polymerization state of the coat basement layer via an extension to a functional intracellular LysM domain that arrests sporulation when coat assembly is initiated improperly. Whereas extracellular LysM domains bind mature peptidoglycan, SpoVID LysM binds to the membrane-bound lipid II peptidoglycan precursor. We propose that improper coat assembly exposes the SpoVID LysM domain, which then sequesters lipid II and prevents cortex assembly. SpoVID defines a widespread group of firmicute proteins with a characteristic N-terminal domain and C-terminal peptidoglycan-binding domains that might combine coat and cortex assembly roles to mediate a developmental checkpoint linking the morphogenesis of two spatially separated supramolecular structures.
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Affiliation(s)
- Thomas Delerue
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael C. Gilmore
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kumaran S. Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA,Lead contact,Correspondence:
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Staphylococcal ClpXP protease targets the cellular antioxidant system to eliminate fitness-compromised cells in stationary phase. Proc Natl Acad Sci U S A 2021; 118:2109671118. [PMID: 34782466 DOI: 10.1073/pnas.2109671118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2021] [Indexed: 01/08/2023] Open
Abstract
The transition from growth to stationary phase is a natural response of bacteria to starvation and stress. When stress is alleviated and more favorable growth conditions return, bacteria resume proliferation without a significant loss in fitness. Although specific adaptations that enhance the persistence and survival of bacteria in stationary phase have been identified, mechanisms that help maintain the competitive fitness potential of nondividing bacterial populations have remained obscure. Here, we demonstrate that staphylococci that enter stationary phase following growth in media supplemented with excess glucose, undergo regulated cell death to maintain the competitive fitness potential of the population. Upon a decrease in extracellular pH, the acetate generated as a byproduct of glucose metabolism induces cytoplasmic acidification and extensive protein damage in nondividing cells. Although cell death ensues, it does not occur as a passive consequence of protein damage. Instead, we demonstrate that the expression and activity of the ClpXP protease is induced, resulting in the degeneration of cellular antioxidant capacity and, ultimately, cell death. Under these conditions, inactivation of either clpX or clpP resulted in the extended survival of unfit cells in stationary phase, but at the cost of maintaining population fitness. Finally, we show that cell death from antibiotics that interfere with bacterial protein synthesis can also be partly ascribed to the corresponding increase in clpP expression and activity. The functional conservation of ClpP in eukaryotes and bacteria suggests that ClpP-dependent cell death and fitness maintenance may be a widespread phenomenon in these domains of life.
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Nerber HN, Sorg JA. The small acid-soluble proteins of Clostridioides difficile are important for UV resistance and serve as a check point for sporulation. PLoS Pathog 2021; 17:e1009516. [PMID: 34496003 PMCID: PMC8452069 DOI: 10.1371/journal.ppat.1009516] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/20/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile is a nosocomial pathogen which causes severe diarrhea and colonic inflammation. C. difficile causes disease in susceptible patients when endospores germinate into the toxin-producing vegetative form. The action of these toxins results in diarrhea and the spread of spores into the hospital and healthcare environments. Thus, the destruction of spores is imperative to prevent disease transmission between patients. However, spores are resilient and survive extreme temperatures, chemical exposure, and UV treatment. This makes their elimination from the environment difficult and perpetuates their spread between patients. In the model spore-forming organism, Bacillus subtilis, the small acid-soluble proteins (SASPs) contribute to these resistances. The SASPs are a family of small proteins found in all endospore-forming organisms, C. difficile included. Although these proteins have high sequence similarity between organisms, the role(s) of the proteins differ. Here, we investigated the role of the main α/β SASPs, SspA and SspB, and two annotated putative SASPs, CDR20291_1130 and CDR20291_3080, in protecting C. difficile spores from environmental insults. We found that SspA is necessary for conferring spore UV resistance, SspB minorly contributes, and the annotated putative SASPs do not contribute to UV resistance. In addition, the SASPs minorly contribute to the resistance of nitrous acid. Surprisingly, the combined deletion of sspA and sspB prevented spore formation. Overall, our data indicate that UV resistance of C. difficile spores is dependent on SspA and that SspA and SspB regulate/serve as a checkpoint for spore formation, a previously unreported function of SASPs.
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Affiliation(s)
- Hailee N. Nerber
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Joseph A. Sorg
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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Abstract
Clostridioides difficile is a leading cause of health care-associated infections worldwide. These infections are transmitted by C. difficile′s metabolically dormant, aerotolerant spore form. Functional spore formation depends on the assembly of two protective layers, a thick layer of modified peptidoglycan known as the cortex layer and a multilayered proteinaceous meshwork known as the coat. We previously identified two spore morphogenetic proteins, SpoIVA and SipL, that are essential for recruiting coat proteins to the developing forespore and making functional spores. While SpoIVA and SipL directly interact, the identities of the proteins they recruit to the forespore remained unknown. Here, we used mass spectrometry-based affinity proteomics to identify proteins that interact with the SpoIVA-SipL complex. These analyses identified the Peptostreptococcaceae family-specific, sporulation-induced bitopic membrane protein CD3457 (renamed SpoVQ) as a protein that interacts with SipL and SpoIVA. Loss of SpoVQ decreased heat-resistant spore formation by ∼5-fold and reduced cortex thickness ∼2-fold; the thinner cortex layer of ΔspoVQ spores correlated with higher levels of spontaneous germination (i.e., in the absence of germinant). Notably, loss of SpoVQ in either spoIVA or sipL mutants prevented cortex synthesis altogether and greatly impaired the localization of a SipL-mCherry fusion protein around the forespore. Thus, SpoVQ is a novel regulator of C. difficile cortex synthesis that appears to link cortex and coat formation. The identification of SpoVQ as a spore morphogenetic protein further highlights how Peptostreptococcaceae family-specific mechanisms control spore formation in C. difficile. IMPORTANCE The Centers for Disease Control has designated Clostridioides difficile as an urgent threat because of its intrinsic antibiotic resistance. C. difficile persists in the presence of antibiotics in part because it makes metabolically dormant spores. While recent work has shown that preventing the formation of infectious spores can reduce C. difficile disease recurrence, more selective antisporulation therapies are needed. The identification of spore morphogenetic factors specific to C. difficile would facilitate the development of such therapies. In this study, we identified SpoVQ (CD3457) as a spore morphogenetic protein specific to the Peptostreptococcaceae family that regulates the formation of C. difficile’s protective spore cortex layer. SpoVQ acts in concert with the known spore coat morphogenetic factors, SpoIVA and SipL, to link formation of the protective coat and cortex layers. These data reveal a novel pathway that could be targeted to prevent the formation of infectious C. difficile spores.
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Diallo M, Kengen SWM, López-Contreras AM. Sporulation in solventogenic and acetogenic clostridia. Appl Microbiol Biotechnol 2021; 105:3533-3557. [PMID: 33900426 PMCID: PMC8102284 DOI: 10.1007/s00253-021-11289-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
The Clostridium genus harbors compelling organisms for biotechnological production processes; while acetogenic clostridia can fix C1-compounds to produce acetate and ethanol, solventogenic clostridia can utilize a wide range of carbon sources to produce commercially valuable carboxylic acids, alcohols, and ketones by fermentation. Despite their potential, the conversion by these bacteria of carbohydrates or C1 compounds to alcohols is not cost-effective enough to result in economically viable processes. Engineering solventogenic clostridia by impairing sporulation is one of the investigated approaches to improve solvent productivity. Sporulation is a cell differentiation process triggered in bacteria in response to exposure to environmental stressors. The generated spores are metabolically inactive but resistant to harsh conditions (UV, chemicals, heat, oxygen). In Firmicutes, sporulation has been mainly studied in bacilli and pathogenic clostridia, and our knowledge of sporulation in solvent-producing or acetogenic clostridia is limited. Still, sporulation is an integral part of the cellular physiology of clostridia; thus, understanding the regulation of sporulation and its connection to solvent production may give clues to improve the performance of solventogenic clostridia. This review aims to provide an overview of the triggers, characteristics, and regulatory mechanism of sporulation in solventogenic clostridia. Those are further compared to the current knowledge on sporulation in the industrially relevant acetogenic clostridia. Finally, the potential applications of spores for process improvement are discussed.Key Points• The regulatory network governing sporulation initiation varies in solventogenic clostridia.• Media composition and cell density are the main triggers of sporulation.• Spores can be used to improve the fermentation process.
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Affiliation(s)
- Mamou Diallo
- Wageningen Food and Biobased Research, Wageningen, The Netherlands.
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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Role of SpoIVA ATPase Motifs during Clostridioides difficile Sporulation. J Bacteriol 2020; 202:JB.00387-20. [PMID: 32817091 PMCID: PMC7549369 DOI: 10.1128/jb.00387-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/04/2020] [Indexed: 01/04/2023] Open
Abstract
The major pathogen Clostridioides difficile depends on its spore form to transmit disease. However, the mechanism by which C. difficile assembles spores remains poorly characterized. We previously showed that binding between the spore morphogenetic proteins SpoIVA and SipL regulates assembly of the protective coat layer around the forespore. In this study, we determined that mutations in the C. difficile SpoIVA ATPase motifs result in relatively minor defects in spore formation, in contrast with Bacillus subtilis. Nevertheless, our data suggest that SipL preferentially recognizes the ATP-bound form of SpoIVA and identify a specific residue in the SipL C-terminal LysM domain that is critical for recognizing the ATP-bound form of SpoIVA. These findings advance our understanding of how SpoIVA-SipL interactions regulate C. difficile spore assembly. The nosocomial pathogen Clostridioides difficile is a spore-forming obligate anaerobe that depends on its aerotolerant spore form to transmit infections. Functional spore formation depends on the assembly of a proteinaceous layer known as the coat around the developing spore. In C. difficile, coat assembly depends on the conserved spore protein SpoIVA and the clostridial-organism-specific spore protein SipL, which directly interact. Mutations that disrupt their interaction cause the coat to mislocalize and impair spore formation. In Bacillus subtilis, SpoIVA is an ATPase that uses ATP hydrolysis to drive its polymerization around the forespore. Loss of SpoIVA ATPase activity impairs B. subtilis SpoIVA encasement of the forespore and activates a quality control mechanism that eliminates these defective cells. Since this mechanism is lacking in C. difficile, we tested whether mutations in the C. difficile SpoIVA ATPase motifs impact functional spore formation. Disrupting C. difficile SpoIVA ATPase motifs resulted in phenotypes that were typically >104-fold less severe than the equivalent mutations in B. subtilis. Interestingly, mutation of ATPase motif residues predicted to abrogate SpoIVA binding to ATP decreased the SpoIVA-SipL interaction, whereas mutation of ATPase motif residues predicted to disrupt ATP hydrolysis but maintain ATP binding enhanced the SpoIVA-SipL interaction. When a sipL mutation known to reduce binding to SpoIVA was combined with a spoIVA mutation predicted to prevent SpoIVA binding to ATP, spore formation was severely exacerbated. Since this phenotype is allele specific, our data imply that SipL recognizes the ATP-bound form of SpoIVA and highlight the importance of this interaction for functional C. difficile spore formation. IMPORTANCE The major pathogen Clostridioides difficile depends on its spore form to transmit disease. However, the mechanism by which C. difficile assembles spores remains poorly characterized. We previously showed that binding between the spore morphogenetic proteins SpoIVA and SipL regulates assembly of the protective coat layer around the forespore. In this study, we determined that mutations in the C. difficile SpoIVA ATPase motifs result in relatively minor defects in spore formation, in contrast with Bacillus subtilis. Nevertheless, our data suggest that SipL preferentially recognizes the ATP-bound form of SpoIVA and identify a specific residue in the SipL C-terminal LysM domain that is critical for recognizing the ATP-bound form of SpoIVA. These findings advance our understanding of how SpoIVA-SipL interactions regulate C. difficile spore assembly.
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Ramisetty BCM, Sudhakari PA. 'Bacterial Programmed Cell Death': cellular altruism or genetic selfism? FEMS Microbiol Lett 2020; 367:5895326. [PMID: 32821912 DOI: 10.1093/femsle/fnaa141] [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: 01/16/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023] Open
Abstract
Cell-dependent propagation of the 'self' is the driver of all species, organisms and even genes. Conceivably, elimination of these entities is caused by cellular death. Then, how can genes that cause the death of the same cell evolve? Programmed cell death (PCD) is the gene-dependent self-inflicted death. In multicellular organisms, PCD of a cell confers fitness to the surviving rest of the organism, which thereby allows the selection of genes responsible for PCD. However, PCD in free-living bacteria is intriguing; the death of the cell is the death of the organism. How can such PCD genes be selected in unicellular organisms? The bacterial PCD in a population is proposed to confer fitness to the surviving kin in the form of sporulation, nutrition, infection-containment and matrix materials. While the cell-centred view leading to propositions of 'altruism' is enticing, the gene-centred view of 'selfism' is neglected. In this opinion piece, we reconceptualize the PCD propositions as genetic selfism (death due to loss/mutation of selfish genes) rather than cellular altruism (death for the conferment of fitness to kin). Within the scope and the available evidence, we opine that some of the PCD-like observations in bacteria seem to be the manifestation of genetic selfism by Restriction-Modification systems and Toxin-Antitoxin systems.
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Affiliation(s)
- Bhaskar Chandra Mohan Ramisetty
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India 613401
| | - Pavithra Anantharaman Sudhakari
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India 613401
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Effects of Atmospheric Plasma Corona Discharges on Soil Bacteria Viability. Microorganisms 2020; 8:microorganisms8050704. [PMID: 32403235 PMCID: PMC7284381 DOI: 10.3390/microorganisms8050704] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 11/17/2022] Open
Abstract
Crop contamination by soil-borne pathogenic microorganisms often leads to serious infection outbreaks. Plant protection requires disinfection of agricultural lands. The chemical and the physical disinfection procedures have several disadvantages, including an irreversible change in the soil ecosystem. Plasma, the "fourth state of matter" is defined as an ionized gas containing an equal number of negatively and positively charged particles. Cold-plasma technology with air or oxygen as the working gas generates reactive oxygen species, which are found to efficiently eradicate bacteria. In this study, we examined the effect of atmospheric plasma corona discharges on soil bacteria viability. Soil that was exposed to plasma for 60 s resulted in bacterial reduction by two orders of magnitude, from 1.1 × 105 to 2.3 × 103 cells g-1 soil. Exposure for a longer period of 5 min did not lead to further significant reduction in bacterial concentration (a final reduction of only 2.5 orders of magnitude). The bacterial viability was evaluated using a colorimetric assay based on the bacterial hydrogenases immediately after exposure and at selected times during 24 h. The result showed no recovery in the bacterial viability. Plasma discharged directly on bacteria that were isolated from the soil resulted in a reduction by four orders of magnitude in the bacterial concentration compared to untreated isolated bacteria: 2.6 × 10-3 and 1.7 × 10-7, respectively. The plasma-resistant bacteria were found to be related to the taxonomic phylum Firmicutes (98.5%) and comprised the taxonomic orders Bacillales (95%) and Clostridiales (2%). To our knowledge, this is the first study of soil bacteria eradication using plasma corona discharges.
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Shen A, Edwards AN, Sarker MR, Paredes-Sabja D. Sporulation and Germination in Clostridial Pathogens. Microbiol Spectr 2019; 7:10.1128/microbiolspec.GPP3-0017-2018. [PMID: 31858953 PMCID: PMC6927485 DOI: 10.1128/microbiolspec.gpp3-0017-2018] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Indexed: 12/14/2022] Open
Abstract
As obligate anaerobes, clostridial pathogens depend on their metabolically dormant, oxygen-tolerant spore form to transmit disease. However, the molecular mechanisms by which those spores germinate to initiate infection and then form new spores to transmit infection remain poorly understood. While sporulation and germination have been well characterized in Bacillus subtilis and Bacillus anthracis, striking differences in the regulation of these processes have been observed between the bacilli and the clostridia, with even some conserved proteins exhibiting differences in their requirements and functions. Here, we review our current understanding of how clostridial pathogens, specifically Clostridium perfringens, Clostridium botulinum, and Clostridioides difficile, induce sporulation in response to environmental cues, assemble resistant spores, and germinate metabolically dormant spores in response to environmental cues. We also discuss the direct relationship between toxin production and spore formation in these pathogens.
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Affiliation(s)
- Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University Medical School, Boston, MA
| | - Adrianne N Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Mahfuzur R Sarker
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR
| | - Daniel Paredes-Sabja
- Department of Gut Microbiota and Clostridia Research Group, Departamento de Ciencias Biolo gicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
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Bressuire-Isoard C, Broussolle V, Carlin F. Sporulation environment influences spore properties in Bacillus: evidence and insights on underlying molecular and physiological mechanisms. FEMS Microbiol Rev 2018; 42:614-626. [DOI: 10.1093/femsre/fuy021] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 05/16/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Christelle Bressuire-Isoard
- UMR408 SQPOV “Sécurité et Qualité des Produits d'Origine Végétale”, INRA–Avignon Université, Centre de Recherche PACA, CS40509, Site Agroparc, 84914 Avignon Cedex 9, France
| | - Véronique Broussolle
- UMR408 SQPOV “Sécurité et Qualité des Produits d'Origine Végétale”, INRA–Avignon Université, Centre de Recherche PACA, CS40509, Site Agroparc, 84914 Avignon Cedex 9, France
| | - Frédéric Carlin
- UMR408 SQPOV “Sécurité et Qualité des Produits d'Origine Végétale”, INRA–Avignon Université, Centre de Recherche PACA, CS40509, Site Agroparc, 84914 Avignon Cedex 9, France
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16
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Cho MS, Jin YJ, Kang BK, Park YK, Kim C, Park DS. Understanding the ontogeny and succession of Bacillus velezensis and B. subtilis subsp. subtilis by focusing on kimchi fermentation. Sci Rep 2018; 8:7045. [PMID: 29728638 PMCID: PMC5935750 DOI: 10.1038/s41598-018-25514-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 04/23/2018] [Indexed: 12/30/2022] Open
Abstract
Bacillus subtilis and B. velezensis are frequently isolated from various niches, including fermented foods, water, and soil. Within the Bacillus subtilis group, B. velezensis and B. subtilis subsp. subtilis have received significant attention as biological resources for biotechnology-associated industries. Nevertheless, radical solutions are urgently needed to identify microbes during their ecological succession to accurately confirm their action at the species or subspecies level in diverse environments, such as fermented materials. Thus, in this study, previously published genome data of the B. subtilis group were compared to exploit species- or subspecies-specific genes for use as improved qPCR targets to detect B. velezensis and B. subtilis subsp. subtilis in kimchi samples. In silico analyses of the selected genes and designed primer sequences, in conjunction with SYBR Green real-time PCR, confirmed the robustness of this newly developed assay. Consequently, this study will allow for new insights into the ontogeny and succession of B. velezensis and B. subtilis subsp. subtilis in various niches. Interestingly, in white kimchi without red pepper powder, neither B. subtilis subsp. subtilis nor B. velezensis was detected.
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Affiliation(s)
- Min Seok Cho
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Yong Ju Jin
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Bo Kyoung Kang
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Yu Kyoung Park
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - ChangKug Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Dong Suk Park
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea.
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Borriss R, Danchin A, Harwood CR, Médigue C, Rocha EP, Sekowska A, Vallenet D. Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement. Microb Biotechnol 2018; 11:3-17. [PMID: 29280348 PMCID: PMC5743806 DOI: 10.1111/1751-7915.13043] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Genome annotation is, nowadays, performed via automatic pipelines that cannot discriminate between right and wrong annotations. Given their importance in increasing the accuracy of the genome annotations of other organisms, it is critical that the annotations of model organisms reflect the current annotation gold standard. The genome of Bacillus subtilis strain 168 was sequenced twenty years ago. Using a combination of inductive, deductive and abductive reasoning, we present a unique, manually curated annotation, essentially based on experimental data. This reveals how this bacterium lives in a plant niche, while carrying a paleome operating system common to Firmicutes and Tenericutes. Dozens of new genomic objects and an extensive literature survey have been included for the sequence available at the INSDC (AccNum AL009126.3). We also propose an extension to Demerec's nomenclature rules that will help investigators connect to this type of curated annotation via the use of common gene names.
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Affiliation(s)
- Rainer Borriss
- Department of PhytomedicineHumboldt‐Universität zu BerlinLentzeallee 55‐5714195BerlinGermany
| | - Antoine Danchin
- Hôpital de la Pitié‐SalpêtrièreInstitute of Cardiometabolism and Nutrition47 Boulevard de l'Hôpital75013ParisFrance
- School of Biomedical SciencesLi Kashing Faculty of MedicineUniversity of Hong Kong21 Sassoon RoadPok Fu LamSAR Hong KongChina
| | - Colin R. Harwood
- The Centre for Bacterial Cell BiologyNewcastle UniversityBaddiley‐Clark BuildingRichardson RoadNewcastle upon TyneNE2 4AXUK
| | - Claudine Médigue
- CEA DRF Genoscope LABGeMCNRS, UMR8030 Génomique MétaboliqueUniversité d'Evry Val d'EssonneUniversité Paris‐SaclayF‐91057EvryFrance
| | - Eduardo P.C. Rocha
- Microbial Evolutionary Genomics UnitInstitut Pasteur28 rue du Docteur Roux75724Paris Cedex 15France
| | - Agnieszka Sekowska
- Hôpital de la Pitié‐SalpêtrièreInstitute of Cardiometabolism and Nutrition47 Boulevard de l'Hôpital75013ParisFrance
| | - David Vallenet
- CEA DRF Genoscope LABGeMCNRS, UMR8030 Génomique MétaboliqueUniversité d'Evry Val d'EssonneUniversité Paris‐SaclayF‐91057EvryFrance
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The Conserved Spore Coat Protein SpoVM Is Largely Dispensable in Clostridium difficile Spore Formation. mSphere 2017; 2:mSphere00315-17. [PMID: 28959733 PMCID: PMC5607322 DOI: 10.1128/msphere.00315-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 08/29/2017] [Indexed: 02/04/2023] Open
Abstract
The spore-forming obligate anaerobe Clostridium difficile is the leading cause of antibiotic-associated diarrheal disease in the United States. When C. difficile spores are ingested by susceptible individuals, they germinate within the gut and transform into vegetative, toxin-secreting cells. During infection, C. difficile must also induce spore formation to survive exit from the host. Since spore formation is essential for transmission, understanding the basic mechanisms underlying sporulation in C. difficile could inform the development of therapeutic strategies targeting spores. In this study, we determine the requirement of the C. difficile homolog of SpoVM, a protein that is essential for spore formation in Bacillus subtilis due to its regulation of coat and cortex formation. We observed that SpoVM plays a minor role in C. difficile spore formation, in contrast with B. subtilis, indicating that this protein would not be a good target for inhibiting spore formation. The spore-forming bacterial pathogen Clostridium difficile is a leading cause of health care-associated infections in the United States. In order for this obligate anaerobe to transmit infection, it must form metabolically dormant spores prior to exiting the host. A key step during this process is the assembly of a protective, multilayered proteinaceous coat around the spore. Coat assembly depends on coat morphogenetic proteins recruiting distinct subsets of coat proteins to the developing spore. While 10 coat morphogenetic proteins have been identified in Bacillus subtilis, only two of these morphogenetic proteins have homologs in the Clostridia: SpoIVA and SpoVM. C. difficile SpoIVA is critical for proper coat assembly and functional spore formation, but the requirement for SpoVM during this process was unknown. Here, we show that SpoVM is largely dispensable for C. difficile spore formation, in contrast with B. subtilis. Loss of C. difficile SpoVM resulted in modest decreases (~3-fold) in heat- and chloroform-resistant spore formation, while morphological defects such as coat detachment from the forespore and abnormal cortex thickness were observed in ~30% of spoVM mutant cells. Biochemical analyses revealed that C. difficile SpoIVA and SpoVM directly interact, similarly to their B. subtilis counterparts. However, in contrast with B. subtilis, C. difficile SpoVM was not essential for SpoIVA to encase the forespore. Since C. difficile coat morphogenesis requires SpoIVA-interacting protein L (SipL), which is conserved exclusively in the Clostridia, but not the more broadly conserved SpoVM, our results reveal another key difference between C. difficile and B. subtilis spore assembly pathways. IMPORTANCE The spore-forming obligate anaerobe Clostridium difficile is the leading cause of antibiotic-associated diarrheal disease in the United States. When C. difficile spores are ingested by susceptible individuals, they germinate within the gut and transform into vegetative, toxin-secreting cells. During infection, C. difficile must also induce spore formation to survive exit from the host. Since spore formation is essential for transmission, understanding the basic mechanisms underlying sporulation in C. difficile could inform the development of therapeutic strategies targeting spores. In this study, we determine the requirement of the C. difficile homolog of SpoVM, a protein that is essential for spore formation in Bacillus subtilis due to its regulation of coat and cortex formation. We observed that SpoVM plays a minor role in C. difficile spore formation, in contrast with B. subtilis, indicating that this protein would not be a good target for inhibiting spore formation.
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