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Fernandez NL, Simmons LA. Two distinct regulatory systems control pulcherrimin biosynthesis in Bacillus subtilis. PLoS Genet 2024; 20:e1011283. [PMID: 38753885 PMCID: PMC11135676 DOI: 10.1371/journal.pgen.1011283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/29/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
Regulation of transcription is a fundamental process that allows bacteria to respond to external stimuli with appropriate timing and magnitude of response. In the soil bacterium Bacillus subtilis, transcriptional regulation is at the core of developmental processes needed for cell survival. Gene expression in cells transitioning from exponential phase to stationary phase is under the control of a group of transcription factors called transition state regulators (TSRs). TSRs influence numerous developmental processes including the decision between biofilm formation and motility, genetic competence, and sporulation, but the extent to which TSRs influence bacterial physiology remains to be fully elucidated. Here, we demonstrate two TSRs, ScoC and AbrB, along with the MarR-family transcription factor PchR negatively regulate production of the iron chelator pulcherrimin in B. subtilis. Genetic analysis of the relationship between the three transcription factors indicate that all are necessary to limit pulcherrimin production during exponential phase and influence the rate and total amount of pulcherrimin produced. Similarly, expression of the pulcherrimin biosynthesis gene yvmC was found to be under control of ScoC, AbrB, and PchR and correlated with the amount of pulcherrimin produced by each background. Lastly, our in vitro data indicate a weak direct role for ScoC in controlling pulcherrimin production along with AbrB and PchR. The layered regulation by two distinct regulatory systems underscores the important role for pulcherrimin in B. subtilis physiology.
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Affiliation(s)
- Nicolas L. Fernandez
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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Hackley RK, Hwang S, Herb JT, Bhanap P, Lam K, Vreugdenhil A, Darnell CL, Pastor MM, Martin JH, Maupin-Furlow JA, Schmid AK. TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii. Mol Microbiol 2024; 121:742-766. [PMID: 38204420 PMCID: PMC11023807 DOI: 10.1111/mmi.15225] [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: 06/09/2023] [Revised: 12/09/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt-loving organism Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. However, the mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that the transcriptional regulator, TrmB, maintains the rod shape in the related species Halobacterium salinarum by activating the expression of enzyme-coding genes in the gluconeogenesis metabolic pathway. In Hbt. salinarum, TrmB-dependent production of glucose moieties is required for cell surface glycoprotein biogenesis. Here, we use a combination of genetics and quantitative phenotyping assays to demonstrate that TrmB is essential for growth under gluconeogenic conditions in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name trmB suppressor, or TbsP (a.k.a. "tablespoon"). TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild-type cell morphology and motility. We use functional genomics and promoter fusion assays to characterize the regulons controlled by each of TrmB and TbsP, including joint regulation of the glucose-dependent transcription of gapII, which encodes an important gluconeogenic enzyme. We conclude that TrmB and TbsP coregulate gluconeogenesis, with downstream impacts on lifestyle transitions in response to nutrients in Hfx. volcanii.
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Affiliation(s)
- Rylee K. Hackley
- Biology Department, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Sungmin Hwang
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Jake T. Herb
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Preeti Bhanap
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Katie Lam
- Biology Department, Duke University, Durham, North Carolina, USA
| | | | | | | | - Johnathan H. Martin
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Amy K. Schmid
- Biology Department, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
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Fernandez NL, Simmons LA. Two Distinct Regulatory Systems Control Pulcherrimin Biosynthesis in Bacillus subtilis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574033. [PMID: 38260623 PMCID: PMC10802322 DOI: 10.1101/2024.01.03.574033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Regulation of transcription is a fundamental process that allows bacteria to respond to external stimuli with appropriate timing and magnitude of response. In the soil bacterium Bacillus subtilis, transcriptional regulation is at the core of developmental processes needed for cell survival. Gene expression in cells transitioning from exponential phase to stationary phase is under the control of a group of transcription factors called transition state regulators (TSRs). TSRs influence numerous developmental processes including the decision between biofilm formation and motility, genetic competence, and sporulation, but the extent to which TSRs influence bacterial physiology remains to be fully elucidated. Here, we demonstrate two TSRs, ScoC and AbrB, along with the MerR-family transcription factor PchR negatively regulate production of the iron chelator pulcherrimin in B. subtilis. Genetic analysis of the relationship between the three transcription factors indicate that all are necessary to limit pulcherrimin production during exponential phase and influence the rate and total amount of pulcherrimin produced. Similarly, expression of the pulcherrimin biosynthesis gene yvmC was found to be under control of ScoC, AbrB, and PchR and correlated with the amount of pulcherrimin produced by each background. Lastly, our in vitro data indicate a weak direct role for ScoC in controlling pulcherrimin production along with AbrB and PchR. The layered regulation by two distinct regulatory systems underscores the important, and somewhat enigmatic, role for pulcherrimin in B. subtilis physiology.
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Affiliation(s)
- Nicolas L. Fernandez
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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Smith P, Schuster M. The fitness benefit of pyoverdine cross-feeding by Pseudomonas protegens Pf-5. Environ Microbiol 2024; 26:e16554. [PMID: 38097191 DOI: 10.1111/1462-2920.16554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023]
Abstract
Under iron-limiting conditions, fluorescent pseudomonads acquire iron from the environment by secreting strain-specific, iron-chelating siderophores termed pyoverdines (PVD). The rhizosphere bacterium Pseudomonas protegens Pf-5 produces its own PVD but also can cross-feed on PVDs produced by other species. Previous work has found that Pf-5 continues to produce its own PVD when allowed to cross-feed, raising questions about the benefit of heterologous PVD utilisation. Here, we investigate this question using a defined, unidirectional P. protegens Pf-5/Pseudomonas aeruginosa PAO1 cross-feeding model. Quantifying the production of PVD in the presence of heterologous PVD produced by PAO1, we show that cross-feeding Pf-5 strains reduce the production of their own PVD, while non-cross-feeding Pf-5 strains increase the production of PVD. Measuring the fitness of cross-feeding and non-cross-feeding Pf-5 strains in triple coculture with PAO1, we find that cross-feeding provides a fitness benefit to Pf-5 when the availability of heterologous PVD is high. We conclude that cross-feeding can reduce the costs of self-PVD production and may thus aid in the colonisation of iron-limited environments that contain compatible siderophores produced by other resident microbes. Taken together, these results expand our understanding of the mechanisms of interspecific competition for iron in microbial communities.
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Affiliation(s)
- Parker Smith
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Martin Schuster
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
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Arora P, Tewary S, Krishnamurthi S, Kumari N. An experimental setup and segmentation method for CFU counting on agar plate for the assessment of drinking water. J Microbiol Methods 2023; 214:106829. [PMID: 37797659 DOI: 10.1016/j.mimet.2023.106829] [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: 07/05/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
Quantification of bacterial colonies on an agar plate is a daily routine for a microbiologist to determine the number of viable microorganisms in the sample. In general, microbiologists perform a visual assessment of bacterial colonies which is time-consuming (takes 2 min per plate), tedious, and subjective. Some automatic counting algorithms are developed that save labour and time, but their results are affected by the non-illumination on an agar plate. To improve this, the present manuscript aims to develop an inexpensive and efficient device to acquire S.aureus images via an automatic counting method using image processing techniques under real laboratory conditions. The proposed method (P_ColonyCount) includes the region of interest extraction and color space transformation followed by filtering, thresholding, morphological operation, distance transform, and watershed technique for the quantification of isolated and overlapping colonies. The present work also shows a comparative study on grayscale, K, and green channels by applying different filter and thresholding techniques on 42 images. The results of all channels were compared with the score provided by the expert (manual count). Out of all the proposed method (P_ColonyCount), the K channel gives the best outcome in comparison with the other two channels (grayscale and green) in terms of precision, recall, and F-measure which are 0.99, 0.99, and 0.99 (2 h), 0.98, 0.99, and 0.98 (4 h), and 0.98, 0.98, 0.98 (6 h) respectively. The execution time of the manual and the proposed method (P_ColonyCount) for 42 images ranges from 19 to 113 s and 15 to 31 s respectively. Apart from this, a user-friendly graphical user interface is also developed for the convenient enumeration of colonies without any expert knowledge/training. The developed imaging device will be useful for researchers and teaching lab settings.
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Affiliation(s)
- Prachi Arora
- Thin Film Coating Facility/Materials Science and Sensor Applications, CSIR-Central Scientific Instruments Organisation (CSIR-CSIO), Sector 30-C, Chandigarh 160030, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suman Tewary
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Advanced Materials and Processes, CSIR-National Metallurgical Laboratory (CSIR-NML), Jamshedpur 831007, India
| | - Srinivasan Krishnamurthi
- MTCC-Gene bank, CSIR-Institute of Microbial Technology (CSIR-IMTECH), Sector 39-A, Chandigarh 160039, India
| | - Neelam Kumari
- Thin Film Coating Facility/Materials Science and Sensor Applications, CSIR-Central Scientific Instruments Organisation (CSIR-CSIO), Sector 30-C, Chandigarh 160030, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Rodrigues C, David GQ, Dos Reis AR. Photograph registration of petri dishes in high quality and image editing of microbiological assays. Int Microbiol 2022; 25:561-570. [PMID: 35305184 DOI: 10.1007/s10123-022-00242-z] [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: 11/19/2021] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 11/25/2022]
Abstract
Science is based on evidence that can be measured or observed through methodical techniques which are expressed in several ways, either quantitatively or qualitatively. Technical photograph becomes one of the most important key tools to disclose experimental results. In microbiological research, several pieces of evidence can be indicated with parameters that are deeply related to culture media; pH and color variation, halo formation, overlay of structures, culture shape, among others. The employment of technical photographs as a strategy of the experimental observation and reliable representation is indispensable. The protocol presented here suggests the production of photographic support in microbiological assays in Petri dishes taken by smartphone to obtain high-quality images, besides showing tools to edit images using PowerPoint. The support is composed of a paper tube with a transparent border, whose reduced light penetration avoiding light reflection over the Petri dishes or the culture media. The edition consists of photograph variation, and in clipping and pasting on uniform backgrounds to provide further detailing. The protocol allowed a standardized photograph collection in high quality, which is ideal for a comparative portrait of microbiological behaviors. The image editing enabled a framework and greater visibility of physical and biological structures in the exhibition of photographs inside the manuscript, such as the removal of noises, background alterations, deformities or irregularities. This protocol is an intelligent and cheap tool to help researcher on the knowledge-obtaining process, and it is applied to different experiments or adapted into the most variable research subjects.
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Affiliation(s)
- Cleverson Rodrigues
- São Paulo State University (UNESP), Postal Code, Ilha Solteira, SP, 15385-000, Brazil.
| | - Grace Queiroz David
- São Paulo State University (UNESP), Postal Code, Ilha Solteira, SP, 15385-000, Brazil.,Mato Grosso State University (UNEMAT), Postal Code, Alta Floresta, MT, 78580-000, Brazil
| | - André Rodrigues Dos Reis
- Department of Biosystems Engineering, São Paulo State Univeristy (UNESP), Rua Domingos da Costa Lopes, 780. Postal Code, Tupã, SP, 17602-496, Brazil
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