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Behera DU, Dixit S, Gaur M, Mishra R, Sahoo RK, Sahoo M, Behera BK, Subudhi BB, Bharat SS, Subudhi E. Sequencing and Characterization of M. morganii Strain UM869: A Comprehensive Comparative Genomic Analysis of Virulence, Antibiotic Resistance, and Functional Pathways. Genes (Basel) 2023; 14:1279. [PMID: 37372459 DOI: 10.3390/genes14061279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/10/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Morganella morganii is a Gram-negative opportunistic Enterobacteriaceae pathogen inherently resistant to colistin. This species causes various clinical and community-acquired infections. This study investigated the virulence factors, resistance mechanisms, functional pathways, and comparative genomic analysis of M. morganii strain UM869 with 79 publicly available genomes. The multidrug resistance strain UM869 harbored 65 genes associated with 30 virulence factors, including efflux pump, hemolysin, urease, adherence, toxin, and endotoxin. Additionally, this strain contained 11 genes related to target alteration, antibiotic inactivation, and efflux resistance mechanisms. Further, the comparative genomic study revealed a high genetic relatedness (98.37%) among the genomes, possibly due to the dissemination of genes between adjoining countries. The core proteome of 79 genomes contains the 2692 core, including 2447 single-copy orthologues. Among them, six were associated with resistance to major antibiotic classes manifested through antibiotic target alteration (PBP3, gyrB) and antibiotic efflux (kpnH, rsmA, qacG; rsmA; CRP). Similarly, 47 core orthologues were annotated to 27 virulence factors. Moreover, mostly core orthologues were mapped to transporters (n = 576), two-component systems (n = 148), transcription factors (n = 117), ribosomes (n = 114), and quorum sensing (n = 77). The presence of diversity in serotypes (type 2, 3, 6, 8, and 11) and variation in gene content adds to the pathogenicity, making them more difficult to treat. This study highlights the genetic similarity among the genomes of M. morganii and their restricted emergence, mostly in Asian countries, in addition to their growing pathogenicity and resistance. However, steps must be taken to undertake large-scale molecular surveillance and to direct suitable therapeutic interventions.
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Affiliation(s)
- Dibyajyoti Uttameswar Behera
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Sangita Dixit
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Mahendra Gaur
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
- Department of Biotechnology & Food Technology, Punjabi University, Patiala 147002, Punjab, India
| | - Rukmini Mishra
- Department of Botany, School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar 761211, Odisha, India
| | - Rajesh Kumar Sahoo
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Maheswata Sahoo
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Bijay Kumar Behera
- College of Fisheries, Rani Lakshmi Bai Central Agricultural University, Gwalior Road, Jhansi 284003, Uttar Pradesh, India
| | - Bharat Bhusan Subudhi
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Sutar Suhas Bharat
- Department of Botany, School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar 761211, Odisha, India
| | - Enketeswara Subudhi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
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Krol E, Werel L, Essen LO, Becker A. Structural and functional diversity of bacterial cyclic nucleotide perception by CRP proteins. MICROLIFE 2023; 4:uqad024. [PMID: 37223727 PMCID: PMC10187061 DOI: 10.1093/femsml/uqad024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
Cyclic AMP (cAMP) is a ubiquitous second messenger synthesized by most living organisms. In bacteria, it plays highly diverse roles in metabolism, host colonization, motility, and many other processes important for optimal fitness. The main route of cAMP perception is through transcription factors from the diverse and versatile CRP-FNR protein superfamily. Since the discovery of the very first CRP protein CAP in Escherichia coli more than four decades ago, its homologs have been characterized in both closely related and distant bacterial species. The cAMP-mediated gene activation for carbon catabolism by a CRP protein in the absence of glucose seems to be restricted to E. coli and its close relatives. In other phyla, the regulatory targets are more diverse. In addition to cAMP, cGMP has recently been identified as a ligand of certain CRP proteins. In a CRP dimer, each of the two cyclic nucleotide molecules makes contacts with both protein subunits and effectuates a conformational change that favors DNA binding. Here, we summarize the current knowledge on structural and physiological aspects of E. coli CAP compared with other cAMP- and cGMP-activated transcription factors, and point to emerging trends in metabolic regulation related to lysine modification and membrane association of CRP proteins.
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Affiliation(s)
- Elizaveta Krol
- Department of Biology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Laura Werel
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Lars Oliver Essen
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Anke Becker
- Corresponding author. Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg. E-mail:
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Acetylation of Cyclic AMP Receptor Protein by Acetyl Phosphate Modulates Mycobacterial Virulence. Microbiol Spectr 2023; 11:e0400222. [PMID: 36700638 PMCID: PMC9927398 DOI: 10.1128/spectrum.04002-22] [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] [Indexed: 01/27/2023] Open
Abstract
The success of Mycobacterium tuberculosis (Mtb) as a pathogen is partly attributed to its ability to sense and respond to dynamic host microenvironments. The cyclic AMP (cAMP) receptor protein (CRP) is closely related to the pathogenicity of Mtb and plays an important role in this process. However, the molecular mechanisms guiding the autoregulation and downstream target genes of CRP while Mtb responds to its environment are not fully understood. Here, it is demonstrated that the acetylation of conserved lysine 193 (K193) within the C-terminal DNA-binding domain of CRP reduces its DNA-binding ability and inhibits transcriptional activity. The reversible acetylation status of CRP K193 was shown to significantly affect mycobacterial growth phenotype, alter the stress response, and regulate the expression of biologically relevant genes using a CRP K193 site-specific mutation. Notably, the acetylation level of K193 decreases under CRP-activating conditions, including the presence of cAMP, low pH, high temperature, and oxidative stress, suggesting that microenvironmental signals can directly regulate CRP K193 acetylation. Both cell- and murine-based infection assays confirmed that CRP K193 is critical to the regulation of Mtb virulence. Furthermore, the acetylation of CRP K193 was shown to be dependent on the intracellular metabolic intermediate acetyl phosphate (AcP), and deacetylation was mediated by NAD+-dependent deacetylases. These findings indicate that AcP-mediated acetylation of CRP K193 decreases CRP activity and negatively regulates the pathogenicity of Mtb. We believe that the underlying mechanisms of cross talk between transcription, posttranslational modifications, and metabolites are a common regulatory mechanism for pathogenic bacteria. IMPORTANCE Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, and the ability of Mtb to survive harsh host conditions has been the subject of intensive research. As a result, we explored the molecular mechanisms guiding downstream target genes of CRP when Mtb responds to its environment. Our study makes a contribution to the literature because we describe the role of acetylated K193 in regulating its binding affinity to target DNA and influencing the virulence of mycobacteria. We discovered that mycobacteria can regulate their pathogenicity through the reversible acetylation of CRP K193 and that this reversible acetylation is mediated by AcP and a NAD+-dependent deacetylase. The regulation of CRPMtb by posttranslational modifications, at the transcriptional level, and by metabolic intermediates contribute to a better understanding of its role in the survival and pathogenicity of mycobacteria.
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Gibson JA, Gebhardt MJ, Santos RERS, Dove SL, Watnick PI. Sequestration of a dual function DNA-binding protein by Vibrio cholerae CRP. Proc Natl Acad Sci U S A 2022; 119:e2210115119. [PMID: 36343262 PMCID: PMC9674212 DOI: 10.1073/pnas.2210115119] [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: 06/17/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022] Open
Abstract
Although the mechanism by which the cyclic AMP receptor protein (CRP) regulates global gene transcription has been intensively studied for decades, new discoveries remain to be made. Here, we report that, during rapid growth, CRP associates with both the well-conserved, dual-function DNA-binding protein peptidase A (PepA) and the cell membrane. These interactions are not present under nutrient-limited growth conditions, due to post-translational modification of three lysines on a single face of CRP. Although coincident DNA binding is rare, dissociation from CRP results in increased PepA occupancy at many chromosomal binding sites and differential regulation of hundreds of genes, including several encoding cyclic dinucleotide phosphodiesterases. We show that PepA represses biofilm formation and activates motility/chemotaxis. We propose a model in which membrane-bound CRP interferes with PepA DNA binding. Under nutrient limitation, PepA is released. Together, CRP and free PepA activate a transcriptional response that impels the bacterium to seek a more hospitable environment. This work uncovers a function for CRP in the sequestration of a regulatory protein. More broadly, it describes a paradigm of bacterial transcriptome modulation through metabolically regulated association of transcription factors with the cell membrane.
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Affiliation(s)
- Jacob A. Gibson
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115
| | - Michael J. Gebhardt
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Renato E. R. S. Santos
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Simon L. Dove
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Paula I. Watnick
- Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
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Forquet R, Nasser W, Reverchon S, Meyer S. Quantitative contribution of the spacer length in the supercoiling-sensitivity of bacterial promoters. Nucleic Acids Res 2022; 50:7287-7297. [PMID: 35776118 PMCID: PMC9303308 DOI: 10.1093/nar/gkac579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 06/15/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
DNA supercoiling acts as a global transcriptional regulator in bacteria, but the promoter sequence or structural determinants controlling its effect remain unclear. It was previously proposed to modulate the torsional angle between the −10 and −35 hexamers, and thereby regulate the formation of the closed-complex depending on the length of the ‘spacer’ between them. Here, we develop a thermodynamic model of this notion based on DNA elasticity, providing quantitative and parameter-free predictions of the relative activation of promoters containing a short versus long spacer when the DNA supercoiling level is varied. The model is tested through an analysis of in vitro and in vivo expression assays of mutant promoters with variable spacer lengths, confirming its accuracy for spacers ranging from 15 to 19 nucleotides, except those of 16 nucleotides where other regulatory mechanisms likely overcome the effect of this specific step. An analysis at the whole-genome scale in Escherichia coli then demonstrates a significant effect of the spacer length on the genomic expression after transient or inheritable superhelical variations, validating the model’s predictions. Altogether, this study shows an example of mechanical constraints associated to promoter binding by RNA Polymerase underpinning a basal and global regulatory mechanism.
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Affiliation(s)
- Raphaël Forquet
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240 MAP, F-69622, France
| | - William Nasser
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240 MAP, F-69622, France
| | - Sylvie Reverchon
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240 MAP, F-69622, France
| | - Sam Meyer
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240 MAP, F-69622, France
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Parejo S, Cabrera JJ, Jiménez-Leiva A, Tomás-Gallardo L, Bedmar EJ, Gates AJ, Mesa S. Fine-Tuning Modulation of Oxidation-Mediated Posttranslational Control of Bradyrhizobium diazoefficiens FixK 2 Transcription Factor. Int J Mol Sci 2022; 23:5117. [PMID: 35563511 PMCID: PMC9104804 DOI: 10.3390/ijms23095117] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/22/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
FixK2 is a CRP/FNR-type transcription factor that plays a central role in a sophisticated regulatory network for the anoxic, microoxic and symbiotic lifestyles of the soybean endosymbiont Bradyrhizobium diazoefficiens. Aside from the balanced expression of the fixK2 gene under microoxic conditions (induced by the two-component regulatory system FixLJ and negatively auto-repressed), FixK2 activity is posttranslationally controlled by proteolysis, and by the oxidation of a singular cysteine residue (C183) near its DNA-binding domain. To simulate the permanent oxidation of FixK2, we replaced C183 for aspartic acid. Purified C183D FixK2 protein showed both low DNA binding and in vitro transcriptional activation from the promoter of the fixNOQP operon, required for respiration under symbiosis. However, in a B. diazoefficiens strain coding for C183D FixK2, expression of a fixNOQP'-'lacZ fusion was similar to that in the wild type, when both strains were grown microoxically. The C183D FixK2 encoding strain also showed a wild-type phenotype in symbiosis with soybeans, and increased fixK2 gene expression levels and FixK2 protein abundance in cells. These two latter observations, together with the global transcriptional profile of the microoxically cultured C183D FixK2 encoding strain, suggest the existence of a finely tuned regulatory strategy to counterbalance the oxidation-mediated inactivation of FixK2 in vivo.
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Affiliation(s)
- Sergio Parejo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (S.P.); (J.J.C.); (A.J.-L.); (E.J.B.)
| | - Juan J. Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (S.P.); (J.J.C.); (A.J.-L.); (E.J.B.)
| | - Andrea Jiménez-Leiva
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (S.P.); (J.J.C.); (A.J.-L.); (E.J.B.)
| | - Laura Tomás-Gallardo
- Proteomics and Biochemistry Unit, Andalusian Centre for Developmental Biology, CSIC-Pablo de Olavide University, 41013 Seville, Spain;
| | - Eulogio J. Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (S.P.); (J.J.C.); (A.J.-L.); (E.J.B.)
| | - Andrew J. Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (S.P.); (J.J.C.); (A.J.-L.); (E.J.B.)
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7
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Abstract
While most small, regulatory RNAs are thought to be “noncoding,” a few have been found to also encode a small protein. Here we describe a 164-nucleotide RNA that encodes a 28-amino acid, amphipathic protein, which interacts with aerobic glycerol-3-phosphate dehydrogenase and increases dehydrogenase activity but also base pairs with two mRNAs to reduce expression. The coding and base-pairing sequences overlap, and the two regulatory functions compete. Bacteria have evolved small RNAs (sRNAs) to regulate numerous biological processes and stress responses. While sRNAs generally are considered to be “noncoding,” a few have been found to also encode a small protein. Here we describe one such dual-function RNA that modulates carbon utilization in Escherichia coli. The 164-nucleotide RNA was previously shown to encode a 28-amino acid protein (denoted AzuC). We discovered the membrane-associated AzuC protein interacts with GlpD, the aerobic glycerol-3-phosphate dehydrogenase, and increases dehydrogenase activity. Overexpression of the RNA encoding AzuC results in a growth defect in glycerol and galactose medium. The defect in galactose medium was still observed for a stop codon mutant derivative, suggesting a second role for the RNA. Consistent with this observation, we found that cadA and galE are repressed by base pairing with the RNA (denoted AzuR). Interestingly, AzuC translation interferes with the observed repression of cadA and galE by the RNA and base pairing interferes with AzuC translation, demonstrating that the translation and base-pairing functions compete.
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Olivar-Casique IB, Medina-Aparicio L, Mayo S, Gama-Martínez Y, Rebollar-Flores JE, Martínez-Batallar G, Encarnación S, Calva E, Hernández-Lucas I. The human bile salt sodium deoxycholate induces metabolic and cell envelope changes in Salmonella Typhi leading to bile resistance. J Med Microbiol 2022; 71. [PMID: 35006066 DOI: 10.1099/jmm.0.001461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Salmonella enterica serovar Typhi (S. Typhi) is the etiological agent of typhoid fever. To establish an infection in the human host, this pathogen must survive the presence of bile salts in the gut and gallbladder.Hypothesis. S. Typhi uses multiple genetic elements to resist the presence of human bile.Aims. To determine the genetic elements that S. Typhi utilizes to tolerate the human bile salt sodium deoxycholate.Methodology. A collection of S. Typhi mutant strains was evaluated for their ability to growth in the presence of sodium deoxycholate and ox-bile. Additionally, transcriptomic and proteomic responses elicited by sodium deoxycholate on S. Typhi cultures were also analysed.Results. Multiple transcriptional factors and some of their dependent genes involved in central metabolism, as well as in cell envelope, are required for deoxycholate resistance.Conclusion. These findings suggest that metabolic adaptation to bile is focused on enhancing energy production to sustain synthesis of cell envelope components exposed to damage by bile salts.
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Affiliation(s)
- Isaac B Olivar-Casique
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Liliana Medina-Aparicio
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Selena Mayo
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Yitzel Gama-Martínez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Javier E Rebollar-Flores
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Gabriel Martínez-Batallar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Sergio Encarnación
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Edmundo Calva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
| | - Ismael Hernández-Lucas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, México
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Rodríguez-Valverde D, León-Montes N, Soria-Bustos J, Martínez-Cruz J, González-Ugalde R, Rivera-Gutiérrez S, González-y-Merchand JA, Rosales-Reyes R, García-Morales L, Hirakawa H, Fox JG, Girón JA, De la Cruz MA, Ares MA. cAMP Receptor Protein Positively Regulates the Expression of Genes Involved in the Biosynthesis of Klebsiella oxytoca Tilivalline Cytotoxin. Front Microbiol 2021; 12:743594. [PMID: 34659176 PMCID: PMC8515920 DOI: 10.3389/fmicb.2021.743594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 08/31/2021] [Indexed: 01/09/2023] Open
Abstract
Klebsiella oxytoca is a resident of the human gut. However, certain K. oxytoca toxigenic strains exist that secrete the nonribosomal peptide tilivalline (TV) cytotoxin. TV is a pyrrolobenzodiazepine that causes antibiotic-associated hemorrhagic colitis (AAHC). The biosynthesis of TV is driven by enzymes encoded by the aroX and NRPS operons. In this study, we determined the effect of environmental signals such as carbon sources, osmolarity, and divalent cations on the transcription of both TV biosynthetic operons. Gene expression was enhanced when bacteria were cultivated in tryptone lactose broth. Glucose, high osmolarity, and depletion of calcium and magnesium diminished gene expression, whereas glycerol increased transcription of both TV biosynthetic operons. The cAMP receptor protein (CRP) is a major transcriptional regulator in bacteria that plays a key role in metabolic regulation. To investigate the role of CRP on the cytotoxicity of K. oxytoca, we compared levels of expression of TV biosynthetic operons and synthesis of TV in wild-type strain MIT 09-7231 and a Δcrp isogenic mutant. In summary, we found that CRP directly activates the transcription of the aroX and NRPS operons and that the absence of CRP reduced cytotoxicity of K. oxytoca on HeLa cells, due to a significant reduction in TV production. This study highlights the importance of the CRP protein in the regulation of virulence genes in enteric bacteria and broadens our knowledge on the regulatory mechanisms of the TV cytotoxin.
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Affiliation(s)
- Diana Rodríguez-Valverde
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Nancy León-Montes
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge Soria-Bustos
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jessica Martínez-Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Ricardo González-Ugalde
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge A. González-y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Roberto Rosales-Reyes
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lázaro García-Morales
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Hidetada Hirakawa
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - James G. Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jorge A. Girón
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel A. De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Miguel A. Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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10
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Discovering the DNA-Binding Consensus of the Thermus thermophilus HB8 Transcriptional Regulator TTHA1359. Int J Mol Sci 2021; 22:ijms221810042. [PMID: 34576207 PMCID: PMC8465061 DOI: 10.3390/ijms221810042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription regulatory proteins, also known as transcription factors, function as molecular switches modulating the first step in gene expression, transcription initiation. Cyclic-AMP receptor proteins (CRPs) and fumarate and nitrate reduction regulators (FNRs) compose the CRP/FNR superfamily of transcription factors, regulating gene expression in response to a spectrum of stimuli. In the present work, a reverse-genetic methodology was applied to the study of TTHA1359, one of four CRP/FNR superfamily transcription factors in the model organism Thermus thermophilus HB8. Restriction Endonuclease Protection, Selection, and Amplification (REPSA) followed by next-generation sequencing techniques and bioinformatic motif discovery allowed identification of a DNA-binding consensus for TTHA1359, 5'-AWTGTRA(N)6TYACAWT-3', which TTHA1359 binds to with high affinity. By bioinformatically mapping the consensus to the T. thermophilus HB8 genome, several potential regulatory TTHA1359-binding sites were identified and validated in vitro. The findings contribute to the knowledge of TTHA1359 regulatory activity within T. thermophilus HB8 and demonstrate the effectiveness of a reverse-genetic methodology in the study of putative transcription factors.
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11
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Zhang Q, Xing C, Kong X, Wang C, Chen X. ChIP-seq Analysis of the Global Regulator Vfr Reveals Novel Insights Into the Biocontrol Agent Pseudomonas protegens FD6. Front Microbiol 2021; 12:667637. [PMID: 34054776 PMCID: PMC8160232 DOI: 10.3389/fmicb.2021.667637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Many Pseudomonas protegens strains produce the antibiotics pyoluteorin (PLT) and 2,4-diacetylphloroglucinol (2,4-DAPG), both of which have antimicrobial properties. The biosynthesis of these metabolites is typically controlled by multiple regulatory factors. Virulence factor regulator (Vfr) is a multifunctional DNA-binding regulator that modulates 2,4-DAPG biosynthesis in P. protegens FD6. However, the mechanism by which Vfr regulates this process remains unclear. In the present study, chromatin immunoprecipitation of FLAG-tagged Vfr and nucleotide sequencing analysis were used to identify 847 putative Vfr binding sites in P. protegens FD6. The consensus P. protegens Vfr binding site predicted from nucleotide sequence alignment is TCACA. The qPCR data showed that Vfr positively regulates the expression of phlF and phlG, and the expression of these genes was characterized in detail. The purified recombinant Vfr bound to an approximately 240-bp fragment within the phlF and phlG upstream regions that harbor putative Vfr consensus sequences. Using electrophoretic mobility shift assays, we localized Vfr binding to a 25-bp fragment that contains part of the Vfr binding region. Vfr binding was eliminated by mutating the TACG and CACA sequences in phlF and phlG, respectively. Taken together, our results show that Vfr directly regulates the expression of the 2,4-DAPG operon by binding to the upstream regions of both the phlF and phlG genes. However, unlike other Vfr-targeted genes, Vfr binding to P. protegens FD6 does not require an intact binding consensus motif. Furthermore, we demonstrated that vfr expression is autoregulated in this bacterium. These results provide novel insights into the regulatory role of Vfr in the biocontrol agent P. protegens.
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Affiliation(s)
- Qingxia Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Chenglin Xing
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xiangwei Kong
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Cheng Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xijun Chen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
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12
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Gárate F, Dokas S, Lanfranco MF, Canavan C, Wang I, Correia JJ, Maillard RA. cAMP is an allosteric modulator of DNA-binding specificity in the cAMP receptor protein from Mycobacterium tuberculosis. J Biol Chem 2021; 296:100480. [PMID: 33640453 PMCID: PMC8026907 DOI: 10.1016/j.jbc.2021.100480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 11/28/2022] Open
Abstract
Allosteric proteins with multiple subunits and ligand-binding sites are central in regulating biological signals. The cAMP receptor protein from Mycobacterium tuberculosis (CRPMTB) is a global regulator of transcription composed of two identical subunits, each one harboring structurally conserved cAMP- and DNA-binding sites. The mechanisms by which these four binding sites are allosterically coupled in CRPMTB remain unclear. Here, we investigate the binding mechanism between CRPMTB and cAMP, and the linkage between cAMP and DNA interactions. Using calorimetric and fluorescence-based assays, we find that cAMP binding is entropically driven and displays negative cooperativity. Fluorescence anisotropy experiments show that apo-CRPMTB forms high-order CRPMTB–DNA oligomers through interactions with nonspecific DNA sequences or preformed CRPMTB–DNA complexes. Moreover, we find that cAMP prevents and reverses the formation of CRPMTB–DNA oligomers, reduces the affinity of CRPMTB for nonspecific DNA sequences, and stabilizes a 1-to-1 CRPMTB–DNA complex, but does not increase the affinity for DNA like in the canonical CRP from Escherichia coli (CRPEcoli). DNA-binding assays as a function of cAMP concentration indicate that one cAMP molecule per homodimer dissociates high-order CRPMTB–DNA oligomers into 1-to-1 complexes. These cAMP-mediated allosteric effects are lost in the double-mutant L47P/E178K found in CRP from Mycobacterium bovis Bacille Calmette-Guérin (CRPBCG). The functional behavior, thermodynamic stability, and dimerization constant of CRPBCG are not due to additive effects of L47P and E178K, indicating long-range interactions between these two sites. Altogether, we provide a previously undescribed archetype of cAMP-mediated allosteric regulation that differs from CRPEcoli, illustrating that structural homology does not imply allosteric homology.
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Affiliation(s)
- Fernanda Gárate
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - Stephen Dokas
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - Maria Fe Lanfranco
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - Clare Canavan
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - Irina Wang
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA
| | - John J Correia
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Rodrigo A Maillard
- Department of Chemistry, Georgetown University, Washington, District of Columbia, USA.
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13
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The HrpG/HrpX Regulon of Xanthomonads-An Insight to the Complexity of Regulation of Virulence Traits in Phytopathogenic Bacteria. Microorganisms 2021; 9:microorganisms9010187. [PMID: 33467109 PMCID: PMC7831014 DOI: 10.3390/microorganisms9010187] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/05/2022] Open
Abstract
Bacteria of the genus Xanthomonas cause a wide variety of economically important diseases in most crops. The virulence of the majority of Xanthomonas spp. is dependent on secretion and translocation of effectors by the type 3 secretion system (T3SS) that is controlled by two master transcriptional regulators HrpG and HrpX. Since their discovery in the 1990s, the two regulators were the focal point of many studies aiming to decipher the regulatory network that controls pathogenicity in Xanthomonas bacteria. HrpG controls the expression of HrpX, which subsequently controls the expression of T3SS apparatus genes and effectors. The HrpG/HrpX regulon is activated in planta and subjected to tight metabolic and genetic regulation. In this review, we cover the advances made in understanding the regulatory networks that control and are controlled by the HrpG/HrpX regulon and their conservation between different Xanthomonas spp.
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14
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Lambrecht SJ, Steglich C, Hess WR. A minimum set of regulators to thrive in the ocean. FEMS Microbiol Rev 2020; 44:232-252. [DOI: 10.1093/femsre/fuaa005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/19/2020] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT
Marine cyanobacteria of the genus Prochlorococcus thrive in high cell numbers throughout the euphotic zones of the world's subtropical and tropical oligotrophic oceans, making them some of the most ecologically relevant photosynthetic microorganisms on Earth. The ecological success of these free-living phototrophs suggests that they are equipped with a regulatory system competent to address many different stress situations. However, Prochlorococcus genomes are compact and streamlined, with the majority encoding only five different sigma factors, five to six two-component systems and eight types of other transcriptional regulators. Here, we summarize the existing information about the functions of these protein regulators, about transcriptomic responses to defined stress conditions, and discuss the current knowledge about riboswitches, RNA-based regulation and the roles of certain metabolites as co-regulators. We focus on the best-studied isolate, Prochlorococcus MED4, but extend to other strains and ecotypes when appropriate, and we include some information gained from metagenomic and metatranscriptomic analyses.
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Affiliation(s)
- S Joke Lambrecht
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Claudia Steglich
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
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15
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Shen BA, Landick R. Transcription of Bacterial Chromatin. J Mol Biol 2019; 431:4040-4066. [PMID: 31153903 PMCID: PMC7248592 DOI: 10.1016/j.jmb.2019.05.041] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/12/2022]
Abstract
Decades of research have probed the interplay between chromatin (genomic DNA associated with proteins and RNAs) and transcription by RNA polymerase (RNAP) in all domains of life. In bacteria, chromatin is compacted into a membrane-free region known as the nucleoid that changes shape and composition depending on the bacterial state. Transcription plays a key role in both shaping the nucleoid and organizing it into domains. At the same time, chromatin impacts transcription by at least five distinct mechanisms: (i) occlusion of RNAP binding; (ii) roadblocking RNAP progression; (iii) constraining DNA topology; (iv) RNA-mediated interactions; and (v) macromolecular demixing and heterogeneity, which may generate phase-separated condensates. These mechanisms are not mutually exclusive and, in combination, mediate gene regulation. Here, we review the current understanding of these mechanisms with a focus on gene silencing by H-NS, transcription coordination by HU, and potential phase separation by Dps. The myriad questions about transcription of bacterial chromatin are increasingly answerable due to methodological advances, enabling a needed paradigm shift in the field of bacterial transcription to focus on regulation of genes in their native state. We can anticipate answers that will define how bacterial chromatin helps coordinate and dynamically regulate gene expression in changing environments.
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Affiliation(s)
- Beth A Shen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States.
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16
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Xiong L, Chan E, Teng JLL, Liu S, Lau SKP, Woo PCY. Malate-Dependent Carbon Utilization Enhances Central Metabolism and Contributes to Biological Fitness of Laribacter hongkongensis via CRP Regulation. Front Microbiol 2019; 10:1991. [PMID: 31555230 PMCID: PMC6722228 DOI: 10.3389/fmicb.2019.01991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/13/2019] [Indexed: 11/15/2022] Open
Abstract
Metabolic adaptation in various environmental niches is crucial for bacterial extracellular survival and intracellular replication during infection. However, the metabolism of carbon/nitrogen sources and related regulatory mechanisms in Laribacter hongkongensis, an asaccharolytic bacterium associated with invasive infections and gastroenteritis, are still unknown. In the present study, we demonstrated that malate can be exploited as a preferred carbon source of L. hongkongensis. Using RNA-sequencing, we compared the transcription profiles of L. hongkongensis cultivated with or without malate supplementation, and observed that malate utilization significantly inhibits the use of alternative carbon sources while enhancing respiratory chain as well as central carbon, sulfur, and urease-mediated nitrogen metabolisms. The tight connection among these important metabolic pathways indicates that L. hongkongensis is capable of integrating information from different metabolism branches to coordinate the expression of metabolic genes and thereby adapt to environmental changing. Furthermore, we identified that a transcription factor, CRP, is repressed by malate-mediated metabolism while negatively regulating the effect of malate on these central metabolic pathways. Remarkably, CRP also responds to various environmental stresses, influences the expression of other transcription factors, and contributes to the biological fitness of L. hongkongensis. The regulatory network and cross-regulation enables the bacteria to make the appropriate metabolic responses and environmental adaptation.
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Affiliation(s)
- Lifeng Xiong
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Elaine Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jade L L Teng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Siguo Liu
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Susanna K P Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, Hong Kong.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, Hong Kong
| | - Patrick C Y Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, Hong Kong.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, Hong Kong
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17
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Feeley BE, Bhardwaj V, McLaughlin PT, Diggs S, Blaha GM, Higgs PI. An amino-terminal threonine/serine motif is necessary for activity of the Crp/Fnr homolog, MrpC and for Myxococcus xanthus developmental robustness. Mol Microbiol 2019; 112:1531-1551. [PMID: 31449700 DOI: 10.1111/mmi.14378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2019] [Indexed: 11/30/2022]
Abstract
The Crp/Fnr family of transcriptional regulators play central roles in transcriptional control of diverse physiological responses, and are activated by a surprising diversity of mechanisms. MrpC is a Crp/Fnr homolog that controls the Myxococcus xanthus developmental program. A long-standing model proposed that MrpC activity is controlled by the Pkn8/Pkn14 serine/threonine kinase cascade, which phosphorylates MrpC on threonine residue(s) located in its extreme amino-terminus. In this study, we demonstrate that a stretch of consecutive threonine and serine residues, T21 T22 S23 S24, is necessary for MrpC activity by promoting efficient DNA binding. Mass spectrometry analysis indicated the TTSS motif is not directly phosphorylated by Pkn14 in vitro but is necessary for efficient Pkn14-dependent phosphorylation on several residues in the remainder of the protein. In an important correction to a long-standing model, we show Pkn8 and Pkn14 kinase activities do not play obvious roles in controlling MrpC activity in wild-type M. xanthus under laboratory conditions. Instead, we propose Pkn14 modulates MrpC DNA binding in response to unknown environmental conditions. Interestingly, substitutions in the TTSS motif caused developmental defects that varied between biological replicates, revealing that MrpC plays a role in promoting a robust developmental phenotype.
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Affiliation(s)
- Brooke E Feeley
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Vidhi Bhardwaj
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hesse, Germany
| | | | - Stephen Diggs
- Department of Biochemistry, University of California, Riverside, Riverside, CA, USA
| | - Gregor M Blaha
- Department of Biochemistry, University of California, Riverside, Riverside, CA, USA
| | - Penelope I Higgs
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
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18
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Phototrophic Lactate Utilization by Rhodopseudomonas palustris Is Stimulated by Coutilization with Additional Substrates. Appl Environ Microbiol 2019; 85:AEM.00048-19. [PMID: 30902855 DOI: 10.1128/aem.00048-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/14/2019] [Indexed: 01/09/2023] Open
Abstract
The phototrophic purple nonsulfur bacterium Rhodopseudomonas palustris is known for its metabolic versatility and is of interest for various industrial and environmental applications. Despite decades of research on R. palustris growth under diverse conditions, patterns of R. palustris growth and carbon utilization with mixtures of carbon substrates remain largely unknown. R. palustris readily utilizes most short-chain organic acids but cannot readily use lactate as a sole carbon source. Here we investigated the influence of mixed-substrate utilization on phototrophic lactate consumption by R. palustris We found that lactate was simultaneously utilized with a variety of other organic acids and glycerol in time frames that were insufficient for R. palustris growth on lactate alone. Thus, lactate utilization by R. palustris was expedited by its coutilization with additional substrates. Separately, experiments using carbon pairs that did not contain lactate revealed acetate-mediated inhibition of glycerol utilization in R. palustris This inhibition was specific to the acetate-glycerol pair, as R. palustris simultaneously utilized acetate or glycerol when either was paired with succinate or lactate. Overall, our results demonstrate that (i) R. palustris commonly employs simultaneous mixed-substrate utilization, (ii) mixed-substrate utilization expands the spectrum of readily utilized organic acids in this species, and (iii) R. palustris has the capacity to exert carbon catabolite control in a substrate-specific manner.IMPORTANCE Bacterial carbon source utilization is frequently assessed using cultures provided single carbon sources. However, the utilization of carbon mixtures by bacteria (i.e., mixed-substrate utilization) is of both fundamental and practical importance; it is central to bacterial physiology and ecology, and it influences the utility of bacteria as biotechnology. Here we investigated mixed-substrate utilization by the model organism Rhodopseudomonas palustris Using mixtures of organic acids and glycerol, we show that R. palustris exhibits an expanded range of usable carbon substrates when provided substrates in mixtures. Specifically, coutilization enabled the prompt consumption of lactate, a substrate that is otherwise not readily used by R. palustris Additionally, we found that R. palustris utilizes acetate and glycerol sequentially, revealing that this species has the capacity to use some substrates in a preferential order. These results provide insights into R. palustris physiology that will aid the use of R. palustris for industrial and commercial applications.
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19
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Sycrp2 Is Essential for Twitching Motility in the Cyanobacterium Synechocystis sp. Strain PCC 6803. J Bacteriol 2018; 200:JB.00436-18. [PMID: 30104238 DOI: 10.1128/jb.00436-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 08/10/2018] [Indexed: 01/13/2023] Open
Abstract
Two cAMP receptor proteins (CRPs), Sycrp1 (encoded by sll1371) and Sycrp2 (encoded by sll1924), exist in the cyanobacterium Synechocystis sp. strain PCC 6803. Previous studies have demonstrated that Sycrp1 has binding affinity for cAMP and is involved in motility by regulating the formation of pili. However, the function of Sycrp2 remains unknown. Here, we report that sycrp2 disruption results in the loss of motility of Synechocystis sp. PCC 6803, and that the phenotype can be recovered by reintroducing the sycrp2 gene into the genome of sycrp2-disrupted mutants. Electron microscopy showed that the sycrp2-disrupted mutant lost the pilus apparatus on the cell surface, resulting in a lack of cell motility. Furthermore, the transcript level of the pilA9-pilA11 operon (essential for cell motility and regulated by the cAMP receptor protein Sycrp1) was markedly decreased in sycrp2-disrupted mutants compared with the wild-type strain. Moreover, yeast two-hybrid analysis and a pulldown assay demonstrated that Sycrp2 interacted with Sycrp1 to form a heterodimer and that Sycrp1 and Sycrp2 interacted with themselves to form homodimers. Gel mobility shift assays revealed that Sycrp1 specifically binds to the upstream region of pilA9 Together, these findings indicate that in Synechocystis sp. PCC 6803, Sycrp2 regulates the formation of pili and cell motility by interacting with Sycrp1.IMPORTANCE cAMP receptor proteins (CRPs) are widely distributed in cyanobacteria and play important roles in regulating gene expression. Although many cyanobacterial species have two cAMP receptor-like proteins, the functional links between them are unknown. Here, we found that Sycrp2 in the cyanobacterium Synechocystis sp. strain PCC 6803 is essential for twitching motility and that it interacts with Sycrp1, a known cAMP receptor protein involved with twitching motility. Our findings indicate that the two cAMP receptor-like proteins in cyanobacteria do not have functional redundancy but rather work together.
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20
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Martínez-Carranza E, Barajas H, Alcaraz LD, Servín-González L, Ponce-Soto GY, Soberón-Chávez G. Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli. Front Microbiol 2018; 9:1059. [PMID: 29910775 PMCID: PMC5992433 DOI: 10.3389/fmicb.2018.01059] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/04/2018] [Indexed: 11/23/2022] Open
Abstract
The definition of bacterial essential genes has been widely pursued using different approaches. Their study has impacted several fields of research such as synthetic biology, the construction of bacteria with minimal chromosomes, the search for new antibiotic targets, or the design of strains with biotechnological applications. Bacterial genomes are mosaics that only share a small subset of gene-sequences (core genome) even among members of the same species. It has been reported that the presence of essential genes is highly variable between closely related bacteria and even among members of the same species, due to the phenomenon known as “non-orthologous gene displacement” that refers to the coding for an essential function by genes with no sequence homology due to horizontal gene transfer (HGT). The existence of dormant forms among bacteria and the high incidence of HGT have been proposed to be driving forces of bacterial evolution, and they might have a role in the low level of conservation of essential genes among related bacteria by non-orthologous gene displacement, but this correlation has not been recognized. The aim of this mini-review is to give a brief overview of the approaches that have been taken to define and study essential genes, and the implications of non-orthologous gene displacement in bacterial evolution, focusing mainly in the case of Escherichia coli. To this end, we reviewed the available literature, and we searched for the presence of the essential genes defined by mutagenesis in the genomes of the 63 best-sequenced E. coli genomes that are available in NCBI database. We could not document specific cases of non-orthologous gene displacement among the E. coli strains analyzed, but we found that the quality of the genome-sequences in the database is not enough to make accurate predictions about the conservation of essential-genes among members of this bacterial species.
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Affiliation(s)
- Enrique Martínez-Carranza
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Hugo Barajas
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis-David Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis Servín-González
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gabriel-Yaxal Ponce-Soto
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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21
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Nosho K, Fukushima H, Asai T, Nishio M, Takamaru R, Kobayashi-Kirschvink KJ, Ogawa T, Hidaka M, Masaki H. cAMP-CRP acts as a key regulator for the viable but non-culturable state in Escherichia coli. MICROBIOLOGY-SGM 2018; 164:410-419. [PMID: 29458560 DOI: 10.1099/mic.0.000618] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A variety of bacteria, including Escherichia coli, are known to enter the viable but non-culturable (VBNC) state under various stress conditions. During this state, cells lose colony-forming activities on conventional agar plates while retaining signs of viability. Diverse environmental stresses including starvation induce the VBNC state. However, little is known about the genetic mechanism inducing this state. Here, we aimed to reveal the genetic determinants of the VBNC state of E. coli. We hypothesized that the VBNC state is a process wherein specific gene products important for colony formation are depleted during the extended period of stress conditions. If so, higher expression of these genes would maintain colony-forming activities, thereby restraining cells from entering the VBNC state. From an E. coli plasmid-encoded ORF library, we identified genes that were responsible for maintaining high colony-forming activities after exposure to starvation condition. Among these, cpdA encoding cAMP phosphodiesterase exhibited higher performance in the maintenance of colony-forming activities. As cpdA overexpression decreases intracellular cAMP, cAMP or its complex with cAMP-receptor protein (CRP) may negatively regulate colony-forming activities under stress conditions. We confirmed this using deletion mutants lacking adenylate cyclase or CRP. These mutants fully maintained colony-forming activities even after a long period of starvation, while wild-type cells lost most of this activity. Thus, we concluded that the lack of cAMP-CRP effectively retains high colony-forming activities, indicating that cAMP-CRP acts as a positive regulator necessary for the induction of the VBNC state in E. coli.
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Affiliation(s)
- Kazuki Nosho
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Hiroko Fukushima
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Takehiro Asai
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Masahiro Nishio
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Reiko Takamaru
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | | | - Tetsuhiro Ogawa
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Makoto Hidaka
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Haruhiko Masaki
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
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Ott E, Kawaguchi Y, Kölbl D, Chaturvedi P, Nakagawa K, Yamagishi A, Weckwerth W, Milojevic T. Proteometabolomic response of Deinococcus radiodurans exposed to UVC and vacuum conditions: Initial studies prior to the Tanpopo space mission. PLoS One 2017; 12:e0189381. [PMID: 29244852 PMCID: PMC5731708 DOI: 10.1371/journal.pone.0189381] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/24/2017] [Indexed: 11/18/2022] Open
Abstract
The multiple extremes resistant bacterium Deinococcus radiodurans is able to withstand harsh conditions of simulated outer space environment. The Tanpopo orbital mission performs a long-term space exposure of D. radiodurans aiming to investigate the possibility of interplanetary transfer of life. The revealing of molecular machinery responsible for survivability of D. radiodurans in the outer space environment can improve our understanding of underlying stress response mechanisms. In this paper, we have evaluated the molecular response of D. radiodurans after the exposure to space-related conditions of UVC irradiation and vacuum. Notably, scanning electron microscopy investigations showed that neither morphology nor cellular integrity of irradiated cells was affected, while integrated proteomic and metabolomic analysis revealed numerous molecular alterations in metabolic and stress response pathways. Several molecular key mechanisms of D. radiodurans, including the tricarboxylic acid cycle, the DNA damage response systems, ROS scavenging systems and transcriptional regulators responded in order to cope with the stressful situation caused by UVC irradiation under vacuum conditions. These results reveal the effectiveness of the integrative proteometabolomic approach as a tool in molecular analysis of microbial stress response caused by space-related factors.
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Affiliation(s)
- Emanuel Ott
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Yuko Kawaguchi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Denise Kölbl
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Kazumichi Nakagawa
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Akihiko Yamagishi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- * E-mail: (TM); (WW)
| | - Tetyana Milojevic
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
- * E-mail: (TM); (WW)
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