1
|
Fernandez M, Callegari EA, Paez MD, González PS, Agostini E. Proteomic analysis to unravel the biochemical mechanisms triggered by Bacillus toyonensis SFC 500-1E under chromium(VI) and phenol stress. Biometals 2023; 36:1081-1108. [PMID: 37209221 DOI: 10.1007/s10534-023-00506-9] [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: 01/17/2023] [Accepted: 04/24/2023] [Indexed: 05/22/2023]
Abstract
Bacillus toyonensis SFC 500-1E is a member of the consortium SFC 500-1 able to remove Cr(VI) and simultaneously tolerate high phenol concentrations. In order to elucidate mechanisms utilized by this strain during the bioremediation process, the differential expression pattern of proteins was analyzed when it grew with or without Cr(VI) (10 mg/L) and Cr(VI) + phenol (10 and 300 mg/L), through two complementary proteomic approaches: gel-based (Gel-LC) and gel-free (shotgun) nanoUHPLC-ESI-MS/MS. A total of 400 differentially expressed proteins were identified, out of which 152 proteins were down-regulated under Cr(VI) and 205 up-regulated in the presence of Cr(VI) + phenol, suggesting the extra effort made by the strain to adapt itself and keep growing when phenol was also added. The major metabolic pathways affected include carbohydrate and energetic metabolism, followed by lipid and amino acid metabolism. Particularly interesting were also ABC transporters and the iron-siderophore transporter as well as transcriptional regulators that can bind metals. Stress-associated global response involving the expression of thioredoxins, SOS response, and chaperones appears to be crucial for the survival of this strain under treatment with both contaminants. This research not only provided a deeper understanding of B. toyonensis SFC 500-1E metabolic role in Cr(VI) and phenol bioremediation process but also allowed us to complete an overview of the consortium SFC 500-1 behavior. This may contribute to an improvement in its use as a bioremediation strategy and also provides a baseline for further research.
Collapse
Affiliation(s)
- Marilina Fernandez
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina.
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina.
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - María D Paez
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - Paola S González
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina
| | - Elizabeth Agostini
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina
| |
Collapse
|
2
|
Arjes HA, Gui H, Porter R, Atolia E, Peters JM, Gross C, Kearns DB, Huang KC. Fatty Acid Synthesis Knockdown Promotes Biofilm Wrinkling and Inhibits Sporulation in Bacillus subtilis. mBio 2022; 13:e0138822. [PMID: 36069446 PMCID: PMC9600695 DOI: 10.1128/mbio.01388-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/05/2022] [Indexed: 02/05/2023] Open
Abstract
Many bacterial species typically live in complex three-dimensional biofilms, yet much remains unknown about differences in essential processes between nonbiofilm and biofilm lifestyles. Here, we created a CRISPR interference (CRISPRi) library of knockdown strains covering all known essential genes in the biofilm-forming Bacillus subtilis strain NCIB 3610 and investigated growth, biofilm colony wrinkling, and sporulation phenotypes of the knockdown library. First, we showed that gene essentiality is largely conserved between liquid and surface growth and between two media. Second, we quantified biofilm colony wrinkling using a custom image analysis algorithm and found that fatty acid synthesis and DNA gyrase knockdown strains exhibited increased wrinkling independent of biofilm matrix gene expression. Third, we designed a high-throughput screen to quantify sporulation efficiency after essential gene knockdown; we found that partial knockdowns of essential genes remained competent for sporulation in a sporulation-inducing medium, but knockdown of essential genes involved in fatty acid synthesis exhibited reduced sporulation efficiency in LB, a medium with generally lower levels of sporulation. We conclude that a subset of essential genes are particularly important for biofilm structure and sporulation/germination and suggest a previously unappreciated and multifaceted role for fatty acid synthesis in bacterial lifestyles and developmental processes. IMPORTANCE For many bacteria, life typically involves growth in dense, three-dimensional communities called biofilms that contain cells with differentiated roles held together by extracellular matrix. To examine how essential gene function varies between vegetative growth and the developmental states of biofilm formation and sporulation, we created and screened a comprehensive library of strains using CRISPRi to knockdown expression of each essential gene in the biofilm-capable Bacillus subtilis strain 3610. High-throughput assays and computational algorithms identified a subset of essential genes involved in biofilm wrinkling and sporulation and indicated that fatty acid synthesis plays important and multifaceted roles in bacterial development.
Collapse
Affiliation(s)
- Heidi A. Arjes
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Haiwen Gui
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Rachel Porter
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA
| | - Esha Atolia
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Carol Gross
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| |
Collapse
|
3
|
van Tilburg AY, Warmer P, van Heel AJ, Sauer U, Kuipers OP. Membrane composition and organization of Bacillus subtilis 168 and its genome-reduced derivative miniBacillus PG10. Microb Biotechnol 2021; 15:1633-1651. [PMID: 34856064 PMCID: PMC9049611 DOI: 10.1111/1751-7915.13978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/13/2021] [Accepted: 11/14/2021] [Indexed: 11/30/2022] Open
Abstract
A form of lateral membrane compartmentalization in bacteria is represented by functional membrane microdomains (FMMs). FMMs are important for various cellular processes and offer application possibilities in microbial biotechnology. We designed a lipidomics method to directly measure relative abundances of lipids in detergent‐resistant and detergent‐sensitive membrane fractions of the model bacterium Bacillus subtilis 168 and the biotechnologically attractive miniBacillus PG10 strain. Our study supports previous work suggesting that cardiolipin and prenol lipids are enriched in FMMs of B. subtilis. Additionally, structural analysis of acyl chains of major phospholipids indicated that FMMs display increased order and thickness compared with the surrounding bilayer. Despite the 36% genome reduction, membrane and FMM integrity are largely preserved in miniBacillus PG10, as supported by analysis of membrane fluidity, flotillin distribution and gene expression data. The novel insights in FMM architecture reported here will contribute to further explore the biological significance of FMMs and the means by which FMMs can be exploited as heterologous production platforms. Moreover, our lipidomics method enables comparative FMM lipid profiling between different bacteria.
Collapse
Affiliation(s)
- Amanda Y van Tilburg
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Philipp Warmer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.,Life Science Zürich PhD Program on Systems Biology, Zürich, Switzerland
| | - Auke J van Heel
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| |
Collapse
|
4
|
Wang M, Yu H, Li X, Shen Z. Single-gene regulated non-spore-forming Bacillus subtilis: Construction, transcriptome responses, and applications for producing enzymes and surfactin. Metab Eng 2020; 62:235-248. [DOI: 10.1016/j.ymben.2020.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 01/01/2023]
|
5
|
Sadiq FA, Flint S, Sakandar HA, He G. Molecular regulation of adhesion and biofilm formation in high and low biofilm producers of Bacillus licheniformis using RNA-Seq. BIOFOULING 2019; 35:143-158. [PMID: 30884970 DOI: 10.1080/08927014.2019.1575960] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 01/14/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
RNA sequencing was used to reveal transcriptional changes during the motile-to-sessile switch in high and low biofilm-forming dairy strains of B. licheniformis isolated from Chinese milk powders. A significant part of the whole gene content was affected during this transition in both strains. In terms of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, seven metabolic pathways were significantly downregulated in the planktonic state compared to the biofilm state in both strains. Lipid and sugar metabolism seemed to play an important role in matrix production. Several genes involved in adhesion, matrix production and the matrix coating were either absent or less expressed in the biofilm state of the low biofilm producer compared to the high biofilm producer. Genes related to sporulation and the production of extracellular polymeric substances were concomitantly expressed in the biofilm state of both strains. These comprehensive insights will be helpful for future research into mechanisms and targets.
Collapse
Affiliation(s)
- Faizan Ahmed Sadiq
- a School of Food Science and Technology , Jiangnan University , Wuxi , PR China
- b College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
| | - Steve Flint
- c School of Food and Nutrition , Massey University , Private Bag 11 222 , Palmerston North , New Zealand
| | - Hafiz Arbab Sakandar
- a School of Food Science and Technology , Jiangnan University , Wuxi , PR China
- d Faculty of Biological Sciences , Quaid-i-Azam University , Islamabad , Pakistan
| | - GuoQing He
- b College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
| |
Collapse
|