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Ogonda LA, Saumonneau A, Dion M, Muge EK, Wamalwa BM, Mulaa FJ, Tellier C. Characterization and engineering of two new GH9 and GH48 cellulases from a Bacillus pumilus isolated from Lake Bogoria. Biotechnol Lett 2021; 43:691-700. [PMID: 33386499 DOI: 10.1007/s10529-020-03056-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVES To search for new alkaliphilic cellulases and to improve their efficiency on crystalline cellulose through molecular engineering RESULTS: Two novel cellulases, BpGH9 and BpGH48, from a Bacillus pumilus strain were identified, cloned and biochemically characterized. BpGH9 is a modular endocellulase belonging to the glycoside hydrolase 9 family (GH9), which contains a catalytic module (GH) and a carbohydrate-binding module belonging to class 3 and subclass c (CBM3c). This enzyme is extremely tolerant to high alkali pH and remains significantly active at pH 10. BpGH48 is an exocellulase, belonging to the glycoside hydrolase 48 family (GH48) and acts on the reducing end of oligo-β1,4 glucanes. A truncated form of BpGH9 and a chimeric fusion with an additional CBM3a module was constructed. The deletion of the CBM3c module results in a significant decline in the catalytic activity. However, fusion of CBM3a, although in a non native position, enhanced the activity of BpGH9 on crystalline cellulose. CONCLUSIONS A new alkaliphilic endocellulase BpGH9, was cloned and engineered as a fusion protein (CBM3a-BpGH9), which led to an improved activity on crystalline cellulose.
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Affiliation(s)
- Lydia A Ogonda
- Université de Nantes, CNRS, UFIP, UMR6286, 2, rue de la Houssinière, 44322, Nantes, France.,Department of Biochemistry, School of Medicine, College of Health Sciences, University of Nairobi, P.O BOX 30197-00100, Nairobi, Kenya.,Department of Medical Biochemistry, School of Medicine, Masinde Muliro University of Science and Technology, P.O BOX 190-50100, Kakamega, Kenya
| | - Amélie Saumonneau
- Université de Nantes, CNRS, UFIP, UMR6286, 2, rue de la Houssinière, 44322, Nantes, France
| | - Michel Dion
- Université de Nantes, IRS2, 44000, Nantes, France
| | - Edward K Muge
- Department of Biochemistry, School of Medicine, College of Health Sciences, University of Nairobi, P.O BOX 30197-00100, Nairobi, Kenya
| | - Benson M Wamalwa
- Department of Chemistry, School of Physical Sciences, College of Biological and Physical Sciences, University of Nairobi, P.O BOX 30197-00100, Nairobi, Kenya
| | - Francis J Mulaa
- Department of Biochemistry, School of Medicine, College of Health Sciences, University of Nairobi, P.O BOX 30197-00100, Nairobi, Kenya
| | - Charles Tellier
- Université de Nantes, CNRS, UFIP, UMR6286, 2, rue de la Houssinière, 44322, Nantes, France.
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Bacillus subtilis Early Colonization of Arabidopsis thaliana Roots Involves Multiple Chemotaxis Receptors. mBio 2016; 7:mBio.01664-16. [PMID: 27899502 PMCID: PMC5137498 DOI: 10.1128/mbio.01664-16] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Colonization of plant roots by Bacillus subtilis is mutually beneficial to plants and bacteria. Plants can secrete up to 30% of their fixed carbon via root exudates, thereby feeding the bacteria, and in return the associated B. subtilis bacteria provide the plant with many growth-promoting traits. Formation of a biofilm on the root by matrix-producing B. subtilis is a well-established requirement for long-term colonization. However, we observed that cells start forming a biofilm only several hours after motile cells first settle on the plant. We also found that intact chemotaxis machinery is required for early root colonization by B. subtilis and for plant protection. Arabidopsis thaliana root exudates attract B. subtilis in vitro, an activity mediated by the two characterized chemoreceptors, McpB and McpC, as well as by the orphan receptor TlpC. Nonetheless, bacteria lacking these chemoreceptors are still able to colonize the root, suggesting that other chemoreceptors might also play a role in this process. These observations suggest that A. thaliana actively recruits B. subtilis through root-secreted molecules, and our results stress the important roles of B. subtilis chemoreceptors for efficient colonization of plants in natural environments. These results demonstrate a remarkable strategy adapted by beneficial rhizobacteria to utilize carbon-rich root exudates, which may facilitate rhizobacterial colonization and a mutualistic association with the host. Bacillus subtilis is a plant growth-promoting rhizobacterium that establishes robust interactions with roots. Many studies have now demonstrated that biofilm formation is required for long-term colonization. However, we observed that motile B. subtilis mediates the first contact with the roots. These cells differentiate into biofilm-producing cells only several hours after the bacteria first contact the root. Our study reveals that intact chemotaxis machinery is required for the bacteria to reach the root. Many, if not all, of the B. subtilis 10 chemoreceptors are involved in the interaction with the plant. These observations stress the importance of root-bacterium interactions in the B. subtilis lifestyle.
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Stepanov VG, Tirumalai MR, Montazari S, Checinska A, Venkateswaran K, Fox GE. Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation. PLoS One 2016; 11:e0157331. [PMID: 27351589 PMCID: PMC4924849 DOI: 10.1371/journal.pone.0157331] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/29/2016] [Indexed: 12/12/2022] Open
Abstract
Bacillus pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. pumilus strains revealed indications of misassembly in the B. pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains.
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Affiliation(s)
- Victor G. Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Saied Montazari
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Aleksandra Checinska
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail:
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