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Peña-Rico MA, Bravo-D HR, Roldan-Sabino C, Castro-Cerritos KV, Huerta-Heredia A, Navarro-Mtz AK. Addition of proteinase K during the culture alter the physiology of Bacillus thuringiensis culture and the cry1Ac, nprX, nprA, and spo0A gene transcription. Antonie van Leeuwenhoek 2021; 115:89-102. [PMID: 34797466 DOI: 10.1007/s10482-021-01683-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/03/2021] [Indexed: 11/30/2022]
Abstract
Bacillus thuringiensis is the major bioinsecticide worldwide produced due to the Cry protein activity. Several studies have been done to improve the cost-productivity relation. The neutral protease A (NprA) is the major extracellular protein massively produced during the stationary phase by this bacterium, contributing to the Cry proteins' degradation. Also, the deletion of aprA and nprA genes enhanced the yield of Cry protein, stabilizing it. Therefore, to increase Cry production, one possibility is to degrade the NprA protease in the culture media. In the present study, proteinase K was used to hydrolyze the NprA to increase Cry production. Proteinase K was added during the exponential growth of B. thuringiensis culture. The bacilli and endospores were measured along all culture, while the Cry protein was measured at the end of the culture. The addition of PK affects the bacilli and spore kinetics positively but negatively to the Cry protein (there is no Cry protein detection). Therefore, the gene expression of the cry1Ac, nprX, nprA, and spo0A was measured. The expression of each gene was followed along all culture. Results demonstrated that PK alters both the transcriptional levels and the expression order of the genes.
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Affiliation(s)
- Miguel A Peña-Rico
- Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México
| | - Humberto R Bravo-D
- División de Estudios de Posgrado, Doctorado en Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México
| | - Crisanto Roldan-Sabino
- Ingeniería en Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México
| | - Karla V Castro-Cerritos
- Instituto de Química Aplicada, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México
| | - Ariana Huerta-Heredia
- Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México.,CONACyT-UNPA, Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México
| | - A Karin Navarro-Mtz
- Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México.
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2
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Expression of
cry
genes in
Bacillus thuringiensis
biotechnology. Appl Microbiol Biotechnol 2019; 103:1617-1626. [DOI: 10.1007/s00253-018-9552-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 01/03/2023]
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3
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Neiditch MB, Capodagli GC, Prehna G, Federle MJ. Genetic and Structural Analyses of RRNPP Intercellular Peptide Signaling of Gram-Positive Bacteria. Annu Rev Genet 2017; 51:311-333. [PMID: 28876981 PMCID: PMC6588834 DOI: 10.1146/annurev-genet-120116-023507] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Bacteria use diffusible chemical messengers, termed pheromones, to coordinate gene expression and behavior among cells in a community by a process known as quorum sensing. Pheromones of many gram-positive bacteria, such as Bacillus and Streptococcus, are small, linear peptides secreted from cells and subsequently detected by sensory receptors such as those belonging to the large family of RRNPP proteins. These proteins are cytoplasmic pheromone receptors sharing a structurally similar pheromone-binding domain that functions allosterically to regulate receptor activity. X-ray crystal structures of prototypical RRNPP members have provided atomic-level insights into their mechanism and regulation by pheromones. This review provides an overview of RRNPP prototype signaling; describes the structure-function of this protein family, which is spread widely among gram-positive bacteria; and suggests approaches to target RRNPP systems in order to manipulate beneficial and harmful bacterial behaviors.
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Affiliation(s)
- Matthew B Neiditch
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey 07103, USA; ,
| | - Glenn C Capodagli
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey 07103, USA; ,
| | - Gerd Prehna
- Center for Structural Biology, Research Resources Center and Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois 60607, USA;
| | - Michael J Federle
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA;
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4
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Chromatography of Quorum Sensing Peptides: An Important Functional Class of the Bacterial Peptidome. Chromatographia 2017. [DOI: 10.1007/s10337-017-3411-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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5
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Hoover SE, Perez AJ, Tsui HCT, Sinha D, Smiley DL, DiMarchi RD, Winkler ME, Lazazzera BA. A new quorum-sensing system (TprA/PhrA) for Streptococcus pneumoniae D39 that regulates a lantibiotic biosynthesis gene cluster. Mol Microbiol 2015; 97:229-43. [PMID: 25869931 DOI: 10.1111/mmi.13029] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2015] [Indexed: 12/20/2022]
Abstract
The Phr peptides of the Bacillus species mediate quorum sensing, but their identification and function in other species of bacteria have not been determined. We have identified a Phr peptide quorum-sensing system (TprA/PhrA) that controls the expression of a lantibiotic gene cluster in the Gram-positive human pathogen, Streptococcus pneumoniae. Lantibiotics are highly modified peptides that are part of the bacteriocin family of antimicrobial peptides. We have characterized the basic mechanism for a Phr-peptide signaling system in S. pneumoniae and found that it induces the expression of the lantibiotic genes when pneumococcal cells are at high density in the presence of galactose, a main sugar of the human nasopharynx, a highly competitive microbial environment. Activity of the Phr peptide system is not seen when pneumococcal cells are grown with glucose, the preferred carbon source and the most prevalent sugar encountered by S. pneumoniae during invasive disease. Thus, the lantibiotic genes are expressed under the control of both cell density signals via the Phr peptide system and nutritional signals from the carbon source present, suggesting that quorum sensing and the lantibiotic machinery may help pneumococcal cells compete for space and resources during colonization of the nasopharynx.
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Affiliation(s)
- Sharon E Hoover
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 609 Charles E. Young Dr. East, 1602 Molecular Science Building, Los Angeles, California, 90095, USA
| | - Amilcar J Perez
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 609 Charles E. Young Dr. East, 1602 Molecular Science Building, Los Angeles, California, 90095, USA
| | - Ho-Ching T Tsui
- Department of Biology, Indiana University Bloomington, Jordan Hall, 1001 East Third Street, Bloomington, Indiana, 47405, USA
| | - Dhriti Sinha
- Department of Biology, Indiana University Bloomington, Jordan Hall, 1001 East Third Street, Bloomington, Indiana, 47405, USA
| | - David L Smiley
- Department of Chemistry, Indiana University Bloomington, 800 E. Kirkwood Avenue, Bloomington, Indiana, 47405, USA
| | - Richard D DiMarchi
- Department of Chemistry, Indiana University Bloomington, 800 E. Kirkwood Avenue, Bloomington, Indiana, 47405, USA
| | - Malcolm E Winkler
- Department of Biology, Indiana University Bloomington, Jordan Hall, 1001 East Third Street, Bloomington, Indiana, 47405, USA
| | - Beth A Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 609 Charles E. Young Dr. East, 1602 Molecular Science Building, Los Angeles, California, 90095, USA
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6
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Jakobs M, Meinhardt F. What renders Bacilli genetically competent? A gaze beyond the model organism. Appl Microbiol Biotechnol 2014; 99:1557-70. [DOI: 10.1007/s00253-014-6316-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 12/20/2022]
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7
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Cabrera R, Rocha J, Flores V, Vázquez-Moreno L, Guarneros G, Olmedo G, Rodríguez-Romero A, de la Torre M. Regulation of sporulation initiation by NprR and its signaling peptide NprRB: molecular recognition and conformational changes. Appl Microbiol Biotechnol 2014; 98:9399-412. [PMID: 25256619 DOI: 10.1007/s00253-014-6094-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/01/2014] [Accepted: 09/10/2014] [Indexed: 12/17/2022]
Abstract
NprR belongs to the RNPP family of quorum-sensing receptors, a group of intracellular regulators activated directly by signaling oligopeptides in Gram-positive bacteria. In Bacillus thuringiensis (Bt), nprR is located in a transcriptional cassette with nprRB that codes for the precursor of the signaling peptide NprRB. NprR is a transcriptional regulator activated by binding of reimported NprRB; however, several reports suggest that NprR also participates in sporulation but the mechanism is unknown. Our in silico results, based on the structural similarity between NprR from Bt and Spo0F-binding Rap proteins from Bacillus subtilis, suggested that NprR could bind Spo0F to modulate the sporulation phosphorelay in Bt. Deletion of nprR-nprRB cassette from Bt caused a delay in sporulation and defective trigger of the Spo0A∼P-activated genes spoIIA and spoIIIG. The DNA-binding domain of NprR was not necessary for this second function, since truncated NprRΔHTH together with nprRB gene was able to restore the sporulation wild type phenotype in the ΔnprR-nprRB mutant. Fluorescence assays showed direct binding between NprR and Spo0F, supporting that NprR is a bifunctional protein. To understand how the NprR activation by NprRB could result in two different functions, we studied the molecular recognition mechanism between the signaling peptide and the receptor. Using synthetic variants of NprRB, we found that SSKPDIVG displayed the highest affinity (Kd = 7.19 nM) toward the recombinant NprR and demonstrated that recognition involves conformational selection. We propose that the peptide concentration in the cell controls the oligomerization state of the NprR-NprRB complex for switching between its two functions.
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Affiliation(s)
- Rosina Cabrera
- Centro de Investigación en Alimentación y Desarrollo A. C., Km 0.6 Carretera a La Victoria, 83304, Hermosillo, Sonora, Mexico
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8
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Lozano Goné AM, Dinorín Téllez Girón J, Jiménez Montejo FE, Hidalgo-Lara ME, López y López VE. Behavior of Transition State Regulator AbrB in Batch Cultures of Bacillus thuringiensis. Curr Microbiol 2014; 69:725-32. [DOI: 10.1007/s00284-014-0650-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/20/2014] [Indexed: 10/25/2022]
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9
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Baker MD, Neiditch MB. Structural basis of response regulator inhibition by a bacterial anti-activator protein. PLoS Biol 2011; 9:e1001226. [PMID: 22215984 PMCID: PMC3246441 DOI: 10.1371/journal.pbio.1001226] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 11/14/2011] [Indexed: 01/26/2023] Open
Abstract
The complex interplay between the response regulator ComA, the anti-activator RapF, and the signaling peptide PhrF controls competence development in Bacillus subtilis. More specifically, ComA drives the expression of genetic competence genes, while RapF inhibits the interaction of ComA with its target promoters. The signaling peptide PhrF accumulates at high cell density and upregulates genetic competence by antagonizing the interaction of RapF and ComA. How RapF functions mechanistically to inhibit ComA activity and how PhrF in turn antagonizes the RapF-ComA interaction were unknown. Here we present the X-ray crystal structure of RapF in complex with the ComA DNA binding domain. Along with biochemical and genetic studies, the X-ray crystal structure reveals how RapF mechanistically regulates ComA function. Interestingly, we found that a RapF surface mimics DNA to block ComA binding to its target promoters. Furthermore, RapF is a monomer either alone or in complex with PhrF, and it undergoes a conformational change upon binding to PhrF, which likely causes the dissociation of ComA from the RapF-ComA complex. Finally, we compare the structure of RapF complexed with the ComA DNA binding domain and the structure of RapH complexed with Spo0F. This comparison reveals that RapF and RapH have strikingly similar overall structures, and that they have evolved different, non-overlapping surfaces to interact with diverse cellular targets. To our knowledge, the data presented here reveal the first atomic level insight into the inhibition of response regulator DNA binding by an anti-activator. Compounds that affect the interaction of Rap and Rap-like proteins with their target domains could serve to regulate medically and commercially important phenotypes in numerous Bacillus species, such as sporulation in B. anthracis and sporulation and the production of Cry protein endotoxin in B. thuringiensis.
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Affiliation(s)
- Melinda D. Baker
- Department of Microbiology and Molecular Genetics, UMDNJ–New Jersey Medical School, Newark, New Jersey, United States of America
| | - Matthew B. Neiditch
- Department of Microbiology and Molecular Genetics, UMDNJ–New Jersey Medical School, Newark, New Jersey, United States of America
- * E-mail:
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10
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Rocha J, Flores V, Cabrera R, Soto-Guzmán A, Granados G, Juaristi E, Guarneros G, de la Torre M. Evolution and some functions of the NprR-NprRB quorum-sensing system in the Bacillus cereus group. Appl Microbiol Biotechnol 2011; 94:1069-78. [PMID: 22159892 DOI: 10.1007/s00253-011-3775-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/17/2011] [Accepted: 11/20/2011] [Indexed: 11/30/2022]
Abstract
Quorum-sensing (QS) is a bacterial mechanism for regulation of gene expression in response to cell density. In Gram-positive bacteria, oligopeptides are the signaling molecules to elicit QS. The RNPP protein family (Rap, NprR, PlcR, and PrgX) are intracellular QS receptors that bind directly to their specific signaling peptide for regulating the transcription of several genes. NprR is the activator of a neutral protease in Bacillus subtilis, and it has been recently related to sporulation, cry genes transcription and extracellular protease activity in strains from the B. cereus group. In the B. thuringiensis genome, downstream nprR, a gene encoding a putative QS signaling propeptide (nprRB) was found. We hypothesized that the nprR and nprRB co-evolved because of their coordinated function in the B. cereus group. A phylogenetic tree of nucleotide sequences of nprR revealed six pherotypes, each corresponding to one putative mature NprRB sequence. The nprR tree does not match the current taxonomic grouping of the B. cereus group or the phylogenetic arrangement obtained when using MLST markers from the same strains. SKPDI and other synthetic peptides encoded in the nprRB gene from B. thuringiensis serovar thuringiensis strain 8741 had effect on temporal regulation of sporulation and expression of a cry1Aa'Z transcriptional fusion, but those peptides that stimulated earlier detection of spores decreased cry1Aa expression suggesting that NprR may either activate or repress the transcription of different genes.
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Affiliation(s)
- Jorge Rocha
- Centro de Investigación en Alimentación y Desarrollo, A. C. Carretera a La Victoria Km 0.6, Hermosillo, Sonora, Mexico
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11
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Mitchell RJ, Lee SK, Kim T, Ghim CM. Microbial linguistics: perspectives and applications of microbial cell-to-cell communication. BMB Rep 2011; 44:1-10. [PMID: 21266100 DOI: 10.5483/bmbrep.2011.44.1.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Inter-cellular communication via diffusible small molecules is a defining character not only of multicellular forms of life but also of single-celled organisms. A large number of bacterial genes are regulated by the change of chemical milieu mediated by the local population density of its own species or others. The cell density-dependent "autoinducer" molecules regulate the expression of those genes involved in genetic competence, biofilm formation and persistence, virulence, sporulation, bioluminescence, antibiotic production, and many others. Recent innovations in recombinant DNA technology and micro-/nano-fluidics systems render the genetic circuitry responsible for cell-to-cell communication feasible to and malleable via synthetic biological approaches. Here we review the current understanding of the molecular biology of bacterial intercellular communication and the novel experimental protocols and platforms used to investigate this phenomenon. A particular emphasis is given to the genetic regulatory circuits that provide the standard building blocks which constitute the syntax of the biochemical communication network. Thus, this review gives focus to the engineering principles necessary for rewiring bacterial chemo-communication for various applications, ranging from population-level gene expression control to the study of host-pathogen interactions.
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Affiliation(s)
- Robert J Mitchell
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
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12
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Rocha-Estrada J, Aceves-Diez AE, Guarneros G, de la Torre M. The RNPP family of quorum-sensing proteins in Gram-positive bacteria. Appl Microbiol Biotechnol 2010; 87:913-23. [PMID: 20502894 DOI: 10.1007/s00253-010-2651-y] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 03/29/2010] [Accepted: 04/20/2010] [Indexed: 11/29/2022]
Abstract
Quorum sensing is one of several mechanisms that bacterial cells use to interact with each other and coordinate certain physiological processes in response to cell density. This mechanism is mediated by extracellular signaling molecules; once a critical threshold concentration has been reached, a target sensor kinase or response regulator is activated (or repressed), facilitating the expression of quorum sensing-dependent genes. Gram-positive bacteria mostly use oligo-peptides as signaling molecules. These cells have a special kind of quorum-sensing systems in which the receptor protein interacts directly with its cognate signaling peptide. The receptors are either Rap phosphatases or transcriptional regulators and integrate the protein family RNPP, from Rap, Npr, PlcR, and PrgX. These quorum-sensing systems control several microbial processes, like sporulation, virulence, biofilm formation, conjugation, and production of extracellular enzymes. Insights of the mechanism of protein-signaling peptide binding as well as the molecular interaction among receptor protein, signaling peptide, and target DNA have changed some earlier perceptions. In spite of the increased knowledge and the potential biotechnological applications of these quorum-sensing systems, few examples on engineering for biotechnological applications have been published. Real applications will arise only when researchers working in applied microbiology and biotechnology are aware of the importance of quorum-sensing systems for health and bioprocess applications.
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Affiliation(s)
- Jorge Rocha-Estrada
- Centro de Investigación en Alimentación y Desarrollo, A. C., Carretera a la Victoria Km. 0.6, 83304, Hermosillo, Sonora, México
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