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Bacillus amyloliquefaciens as an excellent agent for biofertilizer and biocontrol in agriculture: an overview for its mechanisms. Microbiol Res 2022; 259:127016. [DOI: 10.1016/j.micres.2022.127016] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 11/18/2022]
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Neubauer S, Dolgova O, Präg G, Borriss R, Makarewicz O. Substitutional analysis of the C-terminal domain of AbrB revealed its essential role in DNA-binding activity. PLoS One 2014; 9:e97254. [PMID: 24832089 PMCID: PMC4022651 DOI: 10.1371/journal.pone.0097254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/16/2014] [Indexed: 11/28/2022] Open
Abstract
The global transition state regulator AbrB controls more than 100 genes of the Bacillus relatives and is known to interact with varying DNA-sequences. The DNA-binding domain of the AbrB-like proteins was proposed to be located exclusively within the amino-terminal ends. However, the recognition of DNA, and specificity of the binding mechanism, remains elusive still in view of highly differing recognition sites. Here we present a substitutional analysis to examine the role of the carboxy-terminal domain of AbrB from Bacillus subtilis and Bacillus amyloliquefaciens. Our results demonstrate that the carboxy-terminal domains of AbrB affect the DNA-binding properties of the tetrameric AbrB. Most likely, the C-termini are responsible for the cooperative character observed for AbrB interaction with some DNA targets like tycA and phyC.
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Affiliation(s)
- Svetlana Neubauer
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Olga Dolgova
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Gregory Präg
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Rainer Borriss
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
| | - Oliwia Makarewicz
- Institute of Biology, Humboldt University of Berlin, Berlin, Germany
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
- * E-mail:
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Thermodynamic and molecular analysis of the AbrB-binding sites within the phyC-region of Bacillus amyloliquefaciens FZB45. Mol Genet Genomics 2011; 287:111-22. [PMID: 22183144 DOI: 10.1007/s00438-011-0666-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 12/05/2011] [Indexed: 12/16/2022]
Abstract
AbrB is a global regulator of transition state that is known to repress more than 100 genes in Bacillus species. Although AbrB is involved in the regulation of most cellular processes, a conserved binding motif seems to be elusive. Thus, the mechanism of AbrB-mediated transcriptional control is still unclear. In our previous work we identified two separate AbrB-binding sites within phytase gene region (phyC) of Bacillus amyloliquefaciens FZB45, whose integrity is essential for repression. Comparable architecture of AbrB-binding sites is also described for tycA that encodes an antibiotic synthesis enzyme. Considering the size of the AbrB tetramer (56 kDa) and other AbrB binding motifs (~20 to 98 bp) we hypothesized preferred binding positions within both AbrB sites of phyC that exhibit higher affinities to AbrB. Thus, we used surface plasmon resonance (SPR) to study the binding kinetics between AbrB and 40-bp ds-oligonucleotides that were derived from both binding sites. Surface plasmon resonance sensorgrams revealed strong binding kinetics that showed nearly no dissociation and positive cooperativity of the AbrB-DNA interaction to the whole AbrB-binding site 2 and to a small part of AbrB-binding site 1. Using chemically modified DNA we found bases contacting AbrB mainly at one face of the DNA-helix within a core region separated by one helical turn each. High content of modified guanines presented in the control reaction of the KMnO(4) interference assay indicated distortion of the DNA-structure of phyC. In vitro transcription assays and base substitutions within the core region support this idea and the cooperativity of AbrB binding.
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Agervald Å, Zhang X, Stensjö K, Devine E, Lindblad P. CalA, a cyanobacterial AbrB protein, interacts with the upstream region of hypC and acts as a repressor of its transcription in the cyanobacterium Nostoc sp. strain PCC 7120. Appl Environ Microbiol 2010; 76:880-90. [PMID: 20023111 PMCID: PMC2813017 DOI: 10.1128/aem.02521-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2009] [Accepted: 12/04/2009] [Indexed: 12/31/2022] Open
Abstract
The filamentous, heterocystous, nitrogen-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain, depending on growth conditions, up to two hydrogenases directly involved in hydrogen metabolism. HypC is one out of at least seven auxiliary gene products required for synthesis of a functional hydrogenase, specifically involved in the maturation of the large subunit. In this study we present a protein, CalA (Alr0946 in the genome), belonging to the transcription regulator family AbrB, which in protein-DNA assays was found to interact with the upstream region of hypC. Transcriptional investigations showed that calA is cotranscribed with the downstream gene alr0947, which encodes a putative protease from the abortive infection superfamily, Abi. CalA was shown to interact specifically not only with the upstream region of hypC but also with its own upstream region, acting as a repressor on hypC. The bidirectional hydrogenase activity was significantly downregulated when CalA was overexpressed, demonstrating a correlation with the transcription factor, either direct or indirect. In silico studies showed that homologues to both CalA and Alr0947 are highly conserved proteins within cyanobacteria with very similar physical organizations of the corresponding structural genes. Possible functions of the cotranscribed downstream protein Alr0947 are presented. In addition, we present a three-dimensional (3D) model of the DNA binding domain of CalA and putative DNA binding mechanisms are discussed.
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Affiliation(s)
- Åsa Agervald
- Department of Photochemistry and Molecular Science, Ångström Laboratories, Uppsala University, P.O. Box 523, SE-751 20 Uppsala, Sweden, Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, Indiana 47907
| | - Xiaohui Zhang
- Department of Photochemistry and Molecular Science, Ångström Laboratories, Uppsala University, P.O. Box 523, SE-751 20 Uppsala, Sweden, Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, Indiana 47907
| | - Karin Stensjö
- Department of Photochemistry and Molecular Science, Ångström Laboratories, Uppsala University, P.O. Box 523, SE-751 20 Uppsala, Sweden, Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, Indiana 47907
| | - Ellenor Devine
- Department of Photochemistry and Molecular Science, Ångström Laboratories, Uppsala University, P.O. Box 523, SE-751 20 Uppsala, Sweden, Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, Indiana 47907
| | - Peter Lindblad
- Department of Photochemistry and Molecular Science, Ångström Laboratories, Uppsala University, P.O. Box 523, SE-751 20 Uppsala, Sweden, Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, Indiana 47907
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