1
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Heckler C, Vale MG, Canales HDS, Stradiotto GC, Giordano ALPL, Schreiber AZ, Sant'Ana AS. Spore-forming bacteria in gelatin: Characterization, identification by 16S rRNA and MALDI-TOF mass spectrometry (MS), and presence of heat resistance and virulence genes. Int J Food Microbiol 2024; 422:110813. [PMID: 38970997 DOI: 10.1016/j.ijfoodmicro.2024.110813] [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: 02/05/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/08/2024]
Abstract
Gelatin, a versatile protein derived from collagen, is widely used in the food, pharmaceutical and medical sectors. However, bacterial contamination by spore-forming bacteria during gelatin processing represents a significant concern for product safety and quality. In this study, an investigation was carried out to explore the heat and chemical resistance, as well as the identification and characterization of spore-forming bacteria isolated from gelatin processing. The methodologies involved chemical resistance tests with drastic pH in microplates and thermal resistance tests in capillary tubes of various isolates obtained at different processing stages. In addition, phenotypic and genotypic analyses were carried out to characterize the most resistant isolates of spore-forming bacteria. The findings of this study revealed the presence of several species, including Bacillus cereus, Bacillus licheniformis, Bacillus sonorensis, Bacillus subtilis, Geobacillus stearothermophilus, and Clostridium sporogenes, with some isolates exhibiting remarkable chemical and heat resistances. In addition, a significant proportion of the most resistant isolates showed gelatinase activity (n = 19/21; 90.5 %) and the presence of heat resistance (n = 5/21; 23.8 %), and virulence genes (n = 11/21; 52.4 %). The results of this study suggest that interventions should be done in quality control practices and that process parameter adjustments and effective contamination reduction strategies should be implemented through gelatin processing.
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Affiliation(s)
- Caroline Heckler
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Matheus G Vale
- Department of Integrated Systems, Faculty of Mechanical Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Héctor D S Canales
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Graziele C Stradiotto
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Ana Luisa P L Giordano
- Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Angelica Z Schreiber
- Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil.
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2
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Martins D, Nerber HN, Roughton CG, Fasquelle A, Barwinska-Sendra A, Vollmer D, Gray J, Vollmer W, Sorg JA, Salgado PS, Henriques AO, Serrano M. Cleavage of an engulfment peptidoglycan hydrolase by a sporulation signature protease in Clostridioides difficile. Mol Microbiol 2024. [PMID: 38922761 DOI: 10.1111/mmi.15291] [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: 03/27/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
In the model organism Bacillus subtilis, a signaling protease produced in the forespore, SpoIVB, is essential for the activation of the sigma factor σK, which is produced in the mother cell as an inactive pro-protein, pro-σK. SpoIVB has a second function essential to sporulation, most likely during cortex synthesis. The cortex is composed of peptidoglycan (PG) and is essential for the spore's heat resistance and dormancy. Surprisingly, the genome of the intestinal pathogen Clostridioides difficile, in which σK is produced without a pro-sequence, encodes two SpoIVB paralogs, SpoIVB1 and SpoIVB2. Here, we show that spoIVB1 is dispensable for sporulation, while a spoIVB2 in-frame deletion mutant fails to produce heat-resistant spores. The spoIVB2 mutant enters sporulation, undergoes asymmetric division, and completes engulfment of the forespore by the mother cell but fails to synthesize the spore cortex. We show that SpoIIP, a PG hydrolase and part of the engulfasome, the machinery essential for engulfment, is cleaved by SpoIVB2 into an inactive form. Within the engulfasome, the SpoIIP amidase activity generates the substrates for the SpoIID lytic transglycosylase. Thus, following engulfment completion, the cleavage and inactivation of SpoIIP by SpoIVB2 curtails the engulfasome hydrolytic activity, at a time when synthesis of the spore cortex peptidoglycan begins. SpoIVB2 is also required for normal late gene expression in the forespore by a currently unknown mechanism. Together, these observations suggest a role for SpoIVB2 in coordinating late morphological and gene expression events between the forespore and the mother cell.
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Affiliation(s)
- Diogo Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Hailee N Nerber
- Biology Department, Texas A&M University, College Station, Texas, USA
| | - Charlotte G Roughton
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Amaury Fasquelle
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Anna Barwinska-Sendra
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Daniela Vollmer
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Faculty of Medical Sciences, Biosciences Institute, Centre for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Joe Gray
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Waldemar Vollmer
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Faculty of Medical Sciences, Biosciences Institute, Centre for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, UK
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Australia
| | - Joseph A Sorg
- Biology Department, Texas A&M University, College Station, Texas, USA
| | - Paula S Salgado
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Faculty of Medical Sciences, Biosciences Institute, Centre for Bacterial Cell Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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3
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Khanal S, Kim TD, Begyn K, Duverger W, Kramer G, Brul S, Rajkovic A, Devlieghere F, Heyndrickx M, Schymkowitz J, Rousseau F, Broussolle V, Michiels C, Aertsen A. Mechanistic insights into the adaptive evolvability of spore heat resistance in Bacillus cereus sensu lato. Int J Food Microbiol 2024; 418:110709. [PMID: 38663147 DOI: 10.1016/j.ijfoodmicro.2024.110709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/09/2024] [Accepted: 04/13/2024] [Indexed: 05/27/2024]
Abstract
Wet heat treatment is a commonly applied method in the food and medical industries for the inactivation of microorganisms, and bacterial spores in particular. While many studies have delved into the mechanisms underlying wet heat killing and spore resistance, little attention has so far been dedicated to the capacity of spore-forming bacteria to tune their resistance through adaptive evolution. Nevertheless, a recent study from our group revealed that a psychrotrophic strain of the Bacillus cereus sensu lato group (i.e. Bacillus weihenstephanensis LMG 18989) could readily and reproducibly evolve to acquire enhanced spore wet heat resistance without compromising its vegetative cell growth ability at low temperatures. In the current study, we demonstrate that another B. cereus strain (i.e. the mesophilic B. cereus sensu stricto ATCC 14579) can acquire significantly increased spore wet heat resistance as well, and we subjected both the previously and currently obtained mutants to whole genome sequencing. This revealed that five out of six mutants were affected in genes encoding regulators of the spore coat and exosporium pathway (i.e. spoIVFB, sigK and gerE), with three of them being affected in gerE. A synthetically constructed ATCC 14579 ΔgerE mutant likewise yielded spores with increased wet heat resistance, and incurred a compromised spore coat and exosporium. Further investigation revealed significantly increased spore DPA levels and core dehydration as the likely causes for the observed enhanced spore wet heat resistance. Interestingly, deletion of gerE in Bacillus subtilis 168 did not impose increased spore wet heat resistance, underscoring potentially different adaptive evolutionary paths in B. cereus and B. subtilis.
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Affiliation(s)
- Sadhana Khanal
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Tom Dongmin Kim
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Katrien Begyn
- Research Unit Food Microbiology and Food Preservation (FMFP-UGent), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wouter Duverger
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Gertjan Kramer
- Laboratory for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098XH Amsterdam, the Netherlands
| | - Stanley Brul
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098XH Amsterdam, the Netherlands
| | - Andreja Rajkovic
- Research Unit Food Microbiology and Food Preservation (FMFP-UGent), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Frank Devlieghere
- Research Unit Food Microbiology and Food Preservation (FMFP-UGent), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Marc Heyndrickx
- ILVO - Flanders Research Institute for Agriculture, Fisheries and Food, Technology and Food Science, Unit - Food Safety, Melle, Belgium; Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | | | - Chris Michiels
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium..
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4
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Nerber HN, Sorg JA. The small acid-soluble proteins of spore-forming organisms: similarities and differences in function. Anaerobe 2024; 87:102844. [PMID: 38582142 DOI: 10.1016/j.anaerobe.2024.102844] [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: 01/11/2024] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/08/2024]
Abstract
The small acid-soluble proteins are found in all endospore-forming organisms and are a major component of spores. Through their DNA binding capabilities, the SASPs shield the DNA from outside insults (e.g., UV and genotoxic chemicals). The absence of the major SASPs results in spores with reduced viability when exposed to UV light and, in at least one case, the inability to complete sporulation. While the SASPs have been characterized for decades, some evidence suggests that using newer technologies to revisit the roles of the SASPs could reveal novel functions in spore regulation.
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Affiliation(s)
- Hailee N Nerber
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Joseph A Sorg
- Department of Biology, Texas A&M University, College Station, TX, United States.
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5
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Kasu IR, Reyes-Matte O, Bonive-Boscan A, Derman AI, Lopez-Garrido J. Catabolism of germinant amino acids is required to prevent premature spore germination in Bacillus subtilis. mBio 2024; 15:e0056224. [PMID: 38564667 PMCID: PMC11077977 DOI: 10.1128/mbio.00562-24] [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: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Spores of Bacillus subtilis germinate in response to specific germinant molecules that are recognized by receptors in the spore envelope. Germinants signal to the dormant spore that the environment can support vegetative growth, so many germinants, such as alanine and valine, are also essential metabolites. As such, they are also required to build the spore. Here we show that these germinants cause premature germination if they are still present at the latter stages of spore formation and beyond, but that B. subtilis metabolism is configured to prevent this: alanine and valine are catabolized and cleared from wild-type cultures even when alternative carbon and nitrogen sources are present. Alanine and valine accumulate in the spent media of mutants that are unable to catabolize these amino acids, and premature germination is pervasive. Premature germination does not occur if the germinant receptor that responds to alanine and valine is eliminated, or if wild-type strains that are able to catabolize and clear alanine and valine are also present in coculture. Our findings demonstrate that spore-forming bacteria must fine-tune the concentration of any metabolite that can also function as a germinant to a level that is high enough to allow for spore development to proceed, but not so high as to promote premature germination. These results indicate that germinant selection and metabolism are tightly linked, and suggest that germinant receptors evolve in tandem with the catabolic priorities of the spore-forming bacterium. IMPORTANCE Many bacterial species produce dormant cells called endospores, which are not killed by antibiotics or common disinfection practices. Endospores pose critical challenges in the food industry, where endospore contaminations cause food spoilage, and in hospitals, where infections by pathogenic endospore formers threaten the life of millions every year. Endospores lose their resistance properties and can be killed easily when they germinate and exit dormancy. We have discovered that the enzymes that break down the amino acids alanine and valine are critical for the production of stable endospores. If these enzymes are absent, endospores germinate as they are formed or shortly thereafter in response to alanine, which can initiate the germination of many different species' endospores, or to valine. By blocking the activity of alanine dehydrogenase, the enzyme that breaks down alanine and is not present in mammals, it may be possible to inactivate endospores by triggering premature and unproductive germination.
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Affiliation(s)
- Iqra R. Kasu
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | | | - Alan I. Derman
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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6
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Dorbani I, Armengaud J, Carlin F, Duport C. Proteome of spores from biological indicators in sterilization processes: Bacillus pumilus and Bacillus atrophaeus. Proteomics 2024; 24:e2300293. [PMID: 38059874 DOI: 10.1002/pmic.202300293] [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: 07/31/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023]
Abstract
Bacillus atrophaeus and Bacillus pumilus spores are widely used as biological indicators to assess the effectiveness of decontamination procedures. Spores are intricate, multi-layered cellular structures primarily composed of proteins, which significantly contribute to their extreme resistance. Therefore, conducting a comprehensive proteome analysis of spores is crucial to identify the specific proteins conferring spore resistance. Here, we employed a high-throughput shotgun proteomic approach to compare the spore proteomes of B. atrophaeus DSM675 and B. pumilus DSM492, identifying 1312 and 1264 proteins, respectively. While the overall number of proteins found in both strains is roughly equivalent, a closer examination of a subset of 54 spore-specific proteins revealed noteworthy distinctions. Among these 54 proteins, 23 were exclusively detected in one strain, while others were shared between both. Notably, of the 31 proteins detected in both strains, 10 exhibited differential abundance levels, including key coat layer morphogenetic proteins. The exploration of these 54 proteins, considering their presence, absence, and differential abundance, provides a unique molecular signature that may elucidate the differences in sensitivity/resistance profiles between the two strains.
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Affiliation(s)
- Imed Dorbani
- INRAE, Avignon Université, UMR SQPOV, Avignon, France
- Claranor SA, Avignon, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
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7
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Jalil K, Tahara YO, Miyata M. Visualization of Bacillus subtilis spore structure and germination using quick-freeze deep-etch electron microscopy. Microscopy (Oxf) 2024:dfae023. [PMID: 38819330 DOI: 10.1093/jmicro/dfae023] [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: 03/06/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
Bacterial spores, known for their complex and resilient structures, have been the focus of visualization using various methodologies. In this study, we applied quick-freeze and replica electron microscopy techniques, allowing observation of Bacillus subtilis spores in high-contrast and three-dimensional detail. This method facilitated visualization of the spore structure with enhanced resolution and provided new insights into the spores and their germination processes. We identified and described five distinct structures: (i) hair-like structures on the spore surface, (ii) spike formation on the surface of lysozyme-treated spores, (iii) the fractured appearance of the spore cortex during germination, (iv) potential connections between small vesicles and the core membrane and (v) the evolving surface structure of nascent vegetative cells during germination.
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Affiliation(s)
- Kiran Jalil
- Graduate School of Science, Osaka Metropolitan University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Yuhei O Tahara
- Graduate School of Science, Osaka Metropolitan University, Sumiyoshi-ku, Osaka 558-8585, Japan
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka Metropolitan University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Sumiyoshi-ku, Osaka 558-8585, Japan
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka Metropolitan University, Sumiyoshi-ku, Osaka 558-8585, Japan
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8
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Léguillier V, Heddi B, Vidic J. Recent Advances in Aptamer-Based Biosensors for Bacterial Detection. BIOSENSORS 2024; 14:210. [PMID: 38785684 PMCID: PMC11117931 DOI: 10.3390/bios14050210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
The rapid and sensitive detection of pathogenic bacteria is becoming increasingly important for the timely prevention of contamination and the treatment of infections. Biosensors based on nucleic acid aptamers, integrated with optical, electrochemical, and mass-sensitive analytical techniques, have garnered intense interest because of their versatility, cost-efficiency, and ability to exhibit high affinity and specificity in binding bacterial biomarkers, toxins, and whole cells. This review highlights the development of aptamers, their structural characterization, and the chemical modifications enabling optimized recognition properties and enhanced stability in complex biological matrices. Furthermore, recent examples of aptasensors for the detection of bacterial cells, biomarkers, and toxins are discussed. Finally, we explore the barriers to and discuss perspectives on the application of aptamer-based bacterial detection.
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Affiliation(s)
- Vincent Léguillier
- INRAE, AgroParisTech, Micalis Institut, Université Paris-Saclay, UMR 1319, 78350 Jouy-en-Josas, France;
- ENS Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, 91190 Gif-sur-Yvette, France
| | - Brahim Heddi
- ENS Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, 91190 Gif-sur-Yvette, France
| | - Jasmina Vidic
- INRAE, AgroParisTech, Micalis Institut, Université Paris-Saclay, UMR 1319, 78350 Jouy-en-Josas, France;
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9
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Chareyre S, Li X, Anjuwon-Foster BR, Updegrove TB, Clifford S, Brogan AP, Su Y, Zhang L, Chen J, Shroff H, Ramamurthi KS. Cell division machinery drives cell-specific gene activation during differentiation in Bacillus subtilis. Proc Natl Acad Sci U S A 2024; 121:e2400584121. [PMID: 38502707 PMCID: PMC10990147 DOI: 10.1073/pnas.2400584121] [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: 01/10/2024] [Accepted: 02/22/2024] [Indexed: 03/21/2024] Open
Abstract
When faced with starvation, the bacterium Bacillus subtilis transforms itself into a dormant cell type called a "spore". Sporulation initiates with an asymmetric division event, which requires the relocation of the core divisome components FtsA and FtsZ, after which the sigma factor σF is exclusively activated in the smaller daughter cell. Compartment-specific activation of σF requires the SpoIIE phosphatase, which displays a biased localization on one side of the asymmetric division septum and associates with the structural protein DivIVA, but the mechanism by which this preferential localization is achieved is unclear. Here, we isolated a variant of DivIVA that indiscriminately activates σF in both daughter cells due to promiscuous localization of SpoIIE, which was corrected by overproduction of FtsA and FtsZ. We propose that the core components of the redeployed cell division machinery drive the asymmetric localization of DivIVA and SpoIIE to trigger the initiation of the sporulation program.
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Affiliation(s)
- Sylvia Chareyre
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD20892
| | - Xuesong Li
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD20892
- HHMI, Ashburn, VA20147
| | | | - Taylor B. Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD20892
| | - Sarah Clifford
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD20892
| | - Anna P. Brogan
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD20892
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD20892
- HHMI, Ashburn, VA20147
| | - Lixia Zhang
- Advanced Imaging and Microscopy Resource, NIH, Bethesda, MD20892
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, NIH, Bethesda, MD20892
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD20892
- HHMI, Ashburn, VA20147
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10
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Bauda E, Gallet B, Moravcova J, Effantin G, Chan H, Novacek J, Jouneau PH, Rodrigues CDA, Schoehn G, Moriscot C, Morlot C. Ultrastructure of macromolecular assemblies contributing to bacterial spore resistance revealed by in situ cryo-electron tomography. Nat Commun 2024; 15:1376. [PMID: 38355696 PMCID: PMC10867305 DOI: 10.1038/s41467-024-45770-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
Bacterial spores owe their incredible resistance capacities to molecular structures that protect the cell content from external aggressions. Among the determinants of resistance are the quaternary structure of the chromosome and an extracellular shell made of proteinaceous layers (the coat), the assembly of which remains poorly understood. Here, in situ cryo-electron tomography on lamellae generated by cryo-focused ion beam micromachining provides insights into the ultrastructural organization of Bacillus subtilis sporangia. The reconstructed tomograms reveal that early during sporulation, the chromosome in the forespore adopts a toroidal structure harboring 5.5-nm thick fibers. At the same stage, coat proteins at the surface of the forespore form a stack of amorphous or structured layers with distinct electron density, dimensions and organization. By analyzing mutant strains using cryo-electron tomography and transmission electron microscopy on resin sections, we distinguish seven nascent coat regions with different molecular properties, and propose a model for the contribution of coat morphogenetic proteins.
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Affiliation(s)
- Elda Bauda
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Benoit Gallet
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Jana Moravcova
- CEITEC-Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | | | - Helena Chan
- University of Technology Sydney, 2007, Ultimo, NSW, Australia
| | - Jiri Novacek
- CEITEC-Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | | | | | - Guy Schoehn
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | | | - Cecile Morlot
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France.
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11
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Eichenberger P. Spore germination: Two ion channels are better than one. Genes Dev 2024; 38:1-3. [PMID: 38316519 PMCID: PMC10903942 DOI: 10.1101/gad.351554.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Germination is the process by which spores emerge from dormancy. Although spores can remain dormant for decades, the study of germination is an active field of research. In this issue of Genes & Development, Gao and colleagues (pp. 31-45) address a perplexing question: How can a dormant spore initiate germination in response to environmental cues? Three distinct complexes are involved: GerA, a germinant-gated ion channel; 5AF/FigP, a second ion channel required for amplification; and SpoVA, a channel for dipicolinic acid (DPA). DPA release is followed by rehydration of the spore core, thus allowing the resumption of metabolic activity.
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12
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Juneja VK, Osoria M, Altuntas EG, Taneja NK, Thakur S, Kumar GD, Setlow P. Effects of spore purity on the wet heat resistance of Clostridium perfringens, Bacillus cereus and Bacillus subtilis spores. Food Res Int 2024; 177:113904. [PMID: 38225145 DOI: 10.1016/j.foodres.2023.113904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024]
Abstract
Heat resistance of spores of Clostridium perfringens 8238 (Hobbs Serotype 2), Bacillus cereus NCTC 11143 (4810/72), and Bacillus subtilis PS533, an isogenic derivative of strain PS832 (a 168 strain) was determined in ground beef at 95 °C. Spore purification was by centrifugation and washing with sterile distilled water (dH2O), followed by sonication and then Histodenz centrifugation for B. subtilis and C. perfringens, and centrifugation and washing with sterile dH2O followed by Histodenz centrifugation for B. cereus. Bags containing inoculated beef samples were submerged in a temperature-controlled water bath and held at 95 °C for predetermined lengths of time. Surviving spore populations were enumerated by plating on mannitol egg yolk polymyxin agar (MYP) agar plates for B. cereus and B. subtilis, and on tryptose-sulfite-cycloserine agar (TSC) agar plates for C. perfringens. Survivor curves were fitted to linear, linear with tail, and Weibull models using the USDA Integrated Pathogen Modeling Program (IPMP) 2013 software. The Weibull model provided a relatively better fit to the data since the root mean square error (RMSE), mean square error (MSE), sum of squared errors (SSE), and Akaike information criterion (AIC) values were lower than the values obtained using the linear or the linear with tail models. Additionally, the Weibull model accurately predicted the observed D-values at 95 °C for the three spore-formers since the accuracy factor (Af) values ranged from 1.03 to 1.08 and the bias factor (Bf) values were either 1.00 or 1.01. Times at 95 °C to achieve a 3-log reduction decreased from 206 min for C. perfringens spores purified with water washes alone to 191 min with water washes followed by sonication and Histodenz centrifugation, from 7.9 min for B. cereus spores purified with water washes alone to 1.4 min with water washes followed by Histodenz centrifugation, and from 20.6 min for B. subtilis spores purified with water washes alone to 6.7 min for water washes followed by sonication and Histodenz centrifugation. Thermal-death-time values reported in this study will assist food processors to design thermal processes to guard against bacterial spores in cooked foods. In addition, clearly spore purity is an additional factor in spore wet heat resistance, although the cause of this effect is not clear.
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Affiliation(s)
- Vijay K Juneja
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA.
| | - Marangeli Osoria
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA
| | | | - Neetu K Taneja
- Department of Basics and Applied Sciences, NIFTEM, Sonipat 131028, Haryana, India
| | - Sheetal Thakur
- University Centre for Research & Development, UIBT, Chandigarh University, Gharuan-Mohali, Punjab, India
| | - Govindaraj D Kumar
- Center for Food Safety, College of Agriculture and Environmental Sciences, The University of Georgia, Griffin Campus, GA, USA
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA
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13
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Carrasco B, Torres R, Moreno-del Álamo M, Ramos C, Ayora S, Alonso JC. Processing of stalled replication forks in Bacillus subtilis. FEMS Microbiol Rev 2024; 48:fuad065. [PMID: 38052445 PMCID: PMC10804225 DOI: 10.1093/femsre/fuad065] [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: 08/14/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/07/2023] Open
Abstract
Accurate DNA replication and transcription elongation are crucial for preventing the accumulation of unreplicated DNA and genomic instability. Cells have evolved multiple mechanisms to deal with impaired replication fork progression, challenged by both intrinsic and extrinsic impediments. The bacterium Bacillus subtilis, which adopts multiple forms of differentiation and development, serves as an excellent model system for studying the pathways required to cope with replication stress to preserve genomic stability. This review focuses on the genetics, single molecule choreography, and biochemical properties of the proteins that act to circumvent the replicative arrest allowing the resumption of DNA synthesis. The RecA recombinase, its mediators (RecO, RecR, and RadA/Sms) and modulators (RecF, RecX, RarA, RecU, RecD2, and PcrA), repair licensing (DisA), fork remodelers (RuvAB, RecG, RecD2, RadA/Sms, and PriA), Holliday junction resolvase (RecU), nucleases (RnhC and DinG), and translesion synthesis DNA polymerases (PolY1 and PolY2) are key functions required to overcome a replication stress, provided that the fork does not collapse.
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Affiliation(s)
- Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - María Moreno-del Álamo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Cristina Ramos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
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14
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Serrano M, Martins D, Henriques AO. Clostridioides difficile Sporulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:273-314. [PMID: 38175480 DOI: 10.1007/978-3-031-42108-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Some members of the Firmicutes phylum, including many members of the human gut microbiota, are able to differentiate a dormant and highly resistant cell type, the endospore (hereinafter spore for simplicity). Spore-formers can colonize virtually any habitat and, because of their resistance to a wide variety of physical and chemical insults, spores can remain viable in the environment for long periods of time. In the anaerobic enteric pathogen Clostridioides difficile the aetiologic agent is the oxygen-resistant spore, while the toxins produced by actively growing cells are the main cause of the disease symptoms. Here, we review the regulatory circuits that govern entry into sporulation. We also cover the role of spores in the infectious cycle of C. difficile in relation to spore structure and function and the main control points along spore morphogenesis.
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Affiliation(s)
- Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal.
| | - Diogo Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
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15
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Gummelt C, Dupke S, Howaldt S, Zimmermann F, Scholz HC, Laue M, Klee SR. Analysis of Sporulation in Bacillus cereus Biovar anthracis Which Contains an Insertion in the Gene for the Sporulation Factor σ K. Pathogens 2023; 12:1442. [PMID: 38133325 PMCID: PMC10745906 DOI: 10.3390/pathogens12121442] [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: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Bacillus cereus biovar anthracis (Bcbva) is an untypical pathogen causing a fatal anthrax-like disease in a variety of wildlife species in African rainforest areas. In contrast to Bacillus anthracis and most species of the B. cereus group, all strains of the Bcbva cluster contain a 22 kb insertion in the sigK gene which encodes the essential late sporulation sigma factor σK. This insertion is excised during sporulation in a site-specific recombination process resulting in an intact sigK gene and a circular molecule. The sporulation kinetics of two strains each of Bcbva and B. anthracis were compared by the expression analysis of eight sporulation-associated genes, including sigK, using reverse transcriptase quantitative real-time PCR. In addition, morphological sporulation stages were analyzed and quantified by electron microscopy. Our results indicated that the necessary excision of the insertion in Bcbva neither delayed nor inhibited its sporulation. In two spontaneous mutants of Bcbva, the excision of the sigK insertion and sporulation were impeded due to mutations in the spo0A and spoVG regulator genes, respectively. The spo0A frameshift mutation was overcome by intragenic suppression in a revertant which was able to sporulate normally, despite an M171S amino acid exchange in the global regulator Spo0A. A screening of the NCBI database identified further strains of the B. cereus group which possess unrelated insertions in the sigK gene, and two strains containing almost identical insertions at the same gene position. Some of the sigK insertions encode putative prophages, whereas the Bcbva insertion encoded a type I restriction-modification system. The function of these insertions and if they are possibly essential for sporulation remains to be assessed.
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Affiliation(s)
- Constanze Gummelt
- Highly Pathogenic Microorganisms (ZBS 2), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (C.G.); (S.D.); (S.H.); (H.C.S.)
| | - Susann Dupke
- Highly Pathogenic Microorganisms (ZBS 2), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (C.G.); (S.D.); (S.H.); (H.C.S.)
| | - Sabine Howaldt
- Highly Pathogenic Microorganisms (ZBS 2), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (C.G.); (S.D.); (S.H.); (H.C.S.)
| | - Fee Zimmermann
- Epidemiology of Highly Pathogenic Microorganisms (P3), Robert Koch Institute, 13353 Berlin, Germany;
| | - Holger C. Scholz
- Highly Pathogenic Microorganisms (ZBS 2), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (C.G.); (S.D.); (S.H.); (H.C.S.)
| | - Michael Laue
- Advanced Light and Electron Microscopy (ZBS 4), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany;
| | - Silke R. Klee
- Highly Pathogenic Microorganisms (ZBS 2), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (C.G.); (S.D.); (S.H.); (H.C.S.)
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16
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Daly MJ. The scientific revolution that unraveled the astonishing DNA repair capacity of the Deinococcaceae: 40 years on. Can J Microbiol 2023; 69:369-386. [PMID: 37267626 DOI: 10.1139/cjm-2023-0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The family Deinococcaceae exhibits exceptional radiation resistance and possesses all the necessary traits for surviving in radiation-exposed environments. Their survival strategy involves the coupling of metabolic and DNA repair functions, resulting in an extraordinarily efficient homologous repair of DNA double-strand breaks (DSBs) caused by radiation or desiccation. The keys to their survival lie in the hyperaccumulation of manganous (Mn2+)-metabolite antioxidants that protect their DNA repair proteins under extreme oxidative stress and the persistent structural linkage by Holliday junctions of their multiple genome copies per cell that facilitates DSB repair. This coupling of metabolic and DNA repair functions has made polyploid Deinococcus bacteria a useful tool in environmental biotechnology, radiobiology, aging, and planetary protection. The review highlights the groundbreaking contributions of the late Robert G.E. Murray to the field of Deinococcus research and the emergent paradigm-shifting discoveries that revolutionized our understanding of radiation survivability and oxidative stress defense, demonstrating that the proteome, rather than the genome, is the primary target responsible for survivability. These discoveries have led to the commercial development of irradiated vaccines using Deinococcus Mn-peptide antioxidants and have significant implications for various fields.
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Affiliation(s)
- Michael J Daly
- Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Department of Pathology, Bethesda, MD 20814-4799, USA
- Committee on Planetary Protection (CoPP), National Academies of Sciences, Washington, DC 20001, USA
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17
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Hamiot A, Lemy C, Krzewinski F, Faille C, Dubois T. Sporulation conditions influence the surface and adhesion properties of Bacillus subtilis spores. Front Microbiol 2023; 14:1219581. [PMID: 37720141 PMCID: PMC10502511 DOI: 10.3389/fmicb.2023.1219581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/14/2023] [Indexed: 09/19/2023] Open
Abstract
Spore-forming bacteria of the Bacillus subtilis group are responsible for recurrent contamination of processing lines in the food industry which can lead to food spoilage. The persistence of B. subtilis would be due to the high resistance of spores to extreme environmental condition and their propensity to contaminate surfaces. While it is well known that sporulation conditions modulate spore resistance properties, little is known about their effect on surface and adhesion properties. Here, we studied the impact of 13 sporulation conditions on the surface and adhesion properties of B. subtilis 168 spores. We showed that Ca2+ or Mg2+ depletion, lower oxygen availability, acidic pH as well as oxidative stresses during sporulation lead to the release of more hydrophobic and adherent spores. The consequences of these sporulation conditions on crust composition in carbohydrates and proteins were also evaluated. The crust glycans of spores produced in a sporulation medium depleted in Ca2+ or Mg2+ or oxygen-limited conditions were impaired and contained lower amounts of rhamnose and legionaminic acid. In addition, we showed that lower oxygen availability or addition of hydrogen peroxide during sporulation decreases the relative amount of two crust proteins (CgeA and CotY) and the changes observed in these conditions could be due to transcriptional repression of genes involved in crust synthesis in late stationary phase. The fact that sporulation conditions affect the ease with which spores can contaminate surfaces could explain the frequent and recurrent presence of B. subtilis spores in food processing lines.
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Affiliation(s)
- Audrey Hamiot
- Univ. Lille, CNRS, INRAE, Centrale Lille, UMR 8207 - UMET - Unité Matériaux et Transformations, Lille, France
| | - Christelle Lemy
- Univ. Lille, CNRS, INRAE, Centrale Lille, UMR 8207 - UMET - Unité Matériaux et Transformations, Lille, France
| | - Frederic Krzewinski
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Christine Faille
- Univ. Lille, CNRS, INRAE, Centrale Lille, UMR 8207 - UMET - Unité Matériaux et Transformations, Lille, France
| | - Thomas Dubois
- Univ. Lille, CNRS, INRAE, Centrale Lille, UMR 8207 - UMET - Unité Matériaux et Transformations, Lille, France
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18
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Chareyre S, Li X, Anjuwon-Foster BR, Clifford S, Brogan A, Su Y, Shroff H, Ramamurthi KS. Cell division machinery drives cell-specific gene activation during bacterial differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552768. [PMID: 37790399 PMCID: PMC10542145 DOI: 10.1101/2023.08.10.552768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
When faced with starvation, the bacterium Bacillus subtilis transforms itself into a dormant cell type called a "spore". Sporulation initiates with an asymmetric division event, which requires the relocation of the core divisome components FtsA and FtsZ, after which the sigma factor σF is exclusively activated in the smaller daughter cell. Compartment specific activation of σF requires the SpoIIE phosphatase, which displays a biased localization on one side of the asymmetric division septum and associates with the structural protein DivIVA, but the mechanism by which this preferential localization is achieved is unclear. Here, we isolated a variant of DivIVA that indiscriminately activates σF in both daughter cells due to promiscuous localization of SpoIIE, which was corrected by overproduction of FtsA and FtsZ. We propose that a unique feature of the sporulation septum, defined by the cell division machinery, drives the asymmetric localization of DivIVA and SpoIIE to trigger the initiation of the sporulation program.
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Affiliation(s)
- Sylvia Chareyre
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xuesong Li
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Brandon R Anjuwon-Foster
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sarah Clifford
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anna Brogan
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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