1
|
Novak JK, Gardner JG. Current models in bacterial hemicellulase-encoding gene regulation. Appl Microbiol Biotechnol 2024; 108:39. [PMID: 38175245 PMCID: PMC10766802 DOI: 10.1007/s00253-023-12977-4] [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: 12/06/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The discovery and characterization of bacterial carbohydrate-active enzymes is a fundamental component of biotechnology innovation, particularly for renewable fuels and chemicals; however, these studies have increasingly transitioned to exploring the complex regulation required for recalcitrant polysaccharide utilization. This pivot is largely due to the current need to engineer and optimize enzymes for maximal degradation in industrial or biomedical applications. Given the structural simplicity of a single cellulose polymer, and the relatively few enzyme classes required for complete bioconversion, the regulation of cellulases in bacteria has been thoroughly discussed in the literature. However, the diversity of hemicelluloses found in plant biomass and the multitude of carbohydrate-active enzymes required for their deconstruction has resulted in a less comprehensive understanding of bacterial hemicellulase-encoding gene regulation. Here we review the mechanisms of this process and common themes found in the transcriptomic response during plant biomass utilization. By comparing regulatory systems from both Gram-negative and Gram-positive bacteria, as well as drawing parallels to cellulase regulation, our goals are to highlight the shared and distinct features of bacterial hemicellulase-encoding gene regulation and provide a set of guiding questions to improve our understanding of bacterial lignocellulose utilization. KEY POINTS: • Canonical regulatory mechanisms for bacterial hemicellulase-encoding gene expression include hybrid two-component systems (HTCS), extracytoplasmic function (ECF)-σ/anti-σ systems, and carbon catabolite repression (CCR). • Current transcriptomic approaches are increasingly being used to identify hemicellulase-encoding gene regulatory patterns coupled with computational predictions for transcriptional regulators. • Future work should emphasize genetic approaches to improve systems biology tools available for model bacterial systems and emerging microbes with biotechnology potential. Specifically, optimization of Gram-positive systems will require integration of degradative and fermentative capabilities, while optimization of Gram-negative systems will require bolstering the potency of lignocellulolytic capabilities.
Collapse
Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
| |
Collapse
|
2
|
Leigh RJ, McKenna C, McWade R, Lynch B, Walsh F. Comparative genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium from Irish hospitals. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction.
Enterococcus faecium
has emerged as an important nosocomial pathogen, which is increasingly difficult to treat due to the genetic acquisition of vancomycin resistance. Ireland has a recalcitrant vancomycin-resistant bloodstream infection rate compared to other developed countries.
Hypothesis/Gap statement. Vancomycin resistance rates persist amongst
E. faecium
isolates from Irish hospitals. The evolutionary genomics governing these trends have not been fully elucidated.
Methodology. A set of 28 vancomycin-resistant isolates was sequenced to construct a dataset alongside 61 other publicly available Irish genomes. This dataset was extensively analysed using in silico methodologies (comparative genomics, pangenomics, phylogenetics, genotypics and comparative functional analyses) to uncover distinct evolutionary, coevolutionary and clinically relevant population trends.
Results. These results suggest that a stable (in terms of genome size, GC% and number of genes), yet genetically diverse population (in terms of gene content) of
E. faecium
persists in Ireland with acquired resistance arising via plasmid acquisition (vanA) or, to a lesser extent, chromosomal recombination (vanB). Population analysis revealed five clusters with one cluster partitioned into four clades which transcend isolation dates. Pangenomic and recombination analyses revealed an open (whole genome and chromosomal specific) pangenome illustrating a rampant evolutionary pattern. Comparative resistomics and virulomics uncovered distinct chromosomal and mobilomal propensity for multidrug resistance, widespread chromosomal point-mutation-mediated resistance and chromosomally harboured arsenals of virulence factors. Interestingly, a potential difference in biofilm formation strategies was highlighted by coevolutionary analysis, suggesting differential biofilm genotypes between vanA and vanB isolates.
Conclusions. These results highlight the evolutionary history of Irish
E. faecium
isolates and may provide insight into underlying infection dynamics in a clinical setting. Due to the apparent ease of vancomycin resistance acquisition over time, susceptible
E. faecium
should be concurrently reduced in Irish hospitals to mitigate potential resistant infections.
Collapse
Affiliation(s)
- Robert J. Leigh
- Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. Kildare, Ireland
| | - Chloe McKenna
- Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. Kildare, Ireland
| | - Robert McWade
- Department of Microbiology, Mater Misericordiae University Hospital, Eccles St., Dublin 7, D07 R2WY, Ireland
| | - Breda Lynch
- Department of Microbiology, Mater Misericordiae University Hospital, Eccles St., Dublin 7, D07 R2WY, Ireland
| | - Fiona Walsh
- Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. Kildare, Ireland
| |
Collapse
|
3
|
Hasan MK, Dhungel BA, Govind R. Characterization of an operon required for growth on cellobiose in Clostridioides difficile. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001079. [PMID: 34410904 PMCID: PMC8489589 DOI: 10.1099/mic.0.001079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/19/2021] [Indexed: 12/19/2022]
Abstract
Cellobiose metabolism is linked to the virulence properties in numerous bacterial pathogens. Here, we characterized a putative cellobiose PTS operon of Clostridiodes difficile to investigate the role of cellobiose metabolism in C. difficile pathogenesis. Our gene knockout experiments demonstrated that the putative cellobiose operon enables uptake of cellobiose into C. difficile and allows growth when cellobiose is provided as the sole carbon source in minimal medium. Additionally, using reporter gene fusion assays and DNA pulldown experiments, we show that its transcription is regulated by CelR, a novel transcriptional repressor protein, which directly binds to the upstream region of the cellobiose operon to control its expression. We have also identified cellobiose metabolism to play a significant role in C. difficile physiology as observed by the reduction of sporulation efficiency when cellobiose uptake was compromised in the mutant strain. In corroboration to in vitro study findings, our in vivo hamster challenge experiment showed a significant reduction of pathogenicity by the cellobiose mutant strain in both the primary and the recurrent infection model - substantiating the role of cellobiose metabolism in C. difficile pathogenesis.
Collapse
Affiliation(s)
- Md Kamrul Hasan
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Revathi Govind
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| |
Collapse
|
4
|
Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut. Nat Commun 2020; 11:5773. [PMID: 33188211 PMCID: PMC7666174 DOI: 10.1038/s41467-020-19585-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/19/2020] [Indexed: 12/29/2022] Open
Abstract
Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. Here, we test the accuracy of AcGGM within the complex endogenous gut microbiome of pigs, wherein we resolve 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially express AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. However, AcGGM-inclusion also manifests a “butterfly effect”, whereby numerous metabolic changes and interdependent cross-feeding pathways occur in neighboring non-mannanolytic populations that produce short-chain fatty acids. Our findings show how intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with potential to create greater modulatory effects at large. Here, the authors tailor an acetylated galactoglucomannan (AcGGM) fibre from spruce wood to specifically enrich Roseburia and Faecalibacterium - beneficial species which have the enzymatic machinery to breakdown the fibre and generate butyrate. They subsequently perform a piglet feeding trial, metagenomics and metaproteomics, together showing that AcGGM-fed pigs exhibit not only increased Roseburia and Faecalibacterium populations with AcGGM-specific mannan-specific esterases, but also secondary metabolic pathways.
Collapse
|
5
|
Petrova P, Petlichka S, Petrov K. New Bacillus spp. with potential for 2,3-butanediol production from biomass. J Biosci Bioeng 2020; 130:20-28. [PMID: 32169317 DOI: 10.1016/j.jbiosc.2020.02.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/06/2019] [Accepted: 02/07/2020] [Indexed: 10/24/2022]
|
6
|
Panwar D, Kapoor M. Transcriptional analysis of galactomannooligosaccharides utilization by Lactobacillus plantarum WCFS1. Food Microbiol 2020; 86:103336. [DOI: 10.1016/j.fm.2019.103336] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023]
|
7
|
Song Y, Sun W, Fan Y, Xue Y, Liu D, Ma C, Liu W, Mosher W, Luo X, Li Z, Ma W, Zhang T. Galactomannan Degrading Enzymes from the Mannan Utilization Gene Cluster of Alkaliphilic Bacillus sp. N16-5 and Their Synergy on Galactomannan Degradation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:11055-11063. [PMID: 30351049 DOI: 10.1021/acs.jafc.8b03878] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Two glycoside hydrolases encoded by the mannan utilization gene cluster of alkaliphilic Bacillus sp. N16-5 were studied. The recombinant Gal27A (rGal27A) hydrolyzed both galactomannans and oligo-galactomannans to release galactose, while the recombinant Man113A (rMan113A) showed poor activity toward galactomannans, but it hydrolyzed manno-oligosaccharides to release mannose and mannobiose. rGal27A showed synergistic interactions with rMan113A and recombinant β-mannanase ManA (rManA), which is also from Bacillus sp. N16-5, in galactomannan degradation. The synergy degree of rGal27A and rManA on hydrolysis of locust bean gum and guar gum was 1.13 and 2.21, respectively, and that of rGal27A and rMan113A reached 2.00 and 2.68. The main products of galactomannan hydrolyzed by rGal27A and rManA simultaneously were galactose, mannose, mannobiose, and mannotriose, while those of galactomannan hydrolyzed by rGal27A and rMan113A were galactose and mannose. The yields of mannose, mannobiose, and mannotriose dramatically increased compared with the hydrolysis in the presence of rManA or rMan113A alone.
Collapse
Affiliation(s)
- Yajian Song
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China
| | - Wenyuan Sun
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China
| | - Yanli Fan
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology , Chinese Academy of Sciences , Beijing 100101 , China
| | - Duoduo Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China
| | - Cuiping Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China
| | - Wenting Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | - Wesley Mosher
- Department of Food Science and Nutrition , University of Minnesota , St. Paul , Minnesota 55108 , United States
| | - Xuegang Luo
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China
| | - Zhongyuan Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China
| | - Wenjian Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China
| | - Tongcun Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education & Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology , Tianjin University of Science and Technology , Tianjin 300457 , China
| |
Collapse
|
8
|
Song Y, Liu D, Liu M, Yang H, Fan Y, Sun W, Xue Y, Zhang T, Ma Y. Transcriptional regulation of the mannan utilization genes in the alkaliphilic Bacillus sp. N16-5. FEMS Microbiol Lett 2018; 365:4816728. [DOI: 10.1093/femsle/fnx280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/17/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yajian Song
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Duoduo Liu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Mengya Liu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Haixu Yang
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanli Fan
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenyuan Sun
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tongcun Zhang
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| |
Collapse
|
9
|
Chaikaew S, Kanpiengjai A, Intatep J, Unban K, Wongputtisin P, Takata G, Khanongnuch C. X-ray-induced mutation of Bacillus sp. MR10 for manno-oligosaccharides production from copra meal. Prep Biochem Biotechnol 2016; 47:424-433. [DOI: 10.1080/10826068.2016.1252929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Siriporn Chaikaew
- Division of Biotechnology, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Apinun Kanpiengjai
- Division of Biotechnology, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Jenjira Intatep
- Division of Biotechnology, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Kridsada Unban
- Division of Biotechnology, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Pairote Wongputtisin
- Program in Biotechnology, Faculty of Science, Maejo University, Chiang Mai, Thailand
| | - Goro Takata
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan
| | - Chartchai Khanongnuch
- Division of Biotechnology, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
- Cluster of Excellence on Biodiversity based Economy and Society (B-BES), Chiang Mai University, Chiang Mai, Thailand
| |
Collapse
|
10
|
Affiliation(s)
- Prakram Singh Chauhan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, SAS Nagar, Mohali, India and
| | - Naveen Gupta
- Department of Microbiology, Panjab University, Chandigarh, India
| |
Collapse
|
11
|
Murayama S, Ishikawa S, Chumsakul O, Ogasawara N, Oshima T. The Role of α-CTD in the Genome-Wide Transcriptional Regulation of the Bacillus subtilis Cells. PLoS One 2015; 10:e0131588. [PMID: 26154296 PMCID: PMC4495994 DOI: 10.1371/journal.pone.0131588] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 06/02/2015] [Indexed: 11/22/2022] Open
Abstract
The amino acid sequence of the RNA polymerase (RNAP) α-subunit is well conserved throughout the Eubacteria. Its C-terminal domain (α-CTD) is important for the transcriptional regulation of specific promoters in both Escherichia coli and Bacillus subtilis, through interactions with transcription factors and/or a DNA element called the "UP element". However, there is only limited information regarding the α-CTD regulated genes in B. subtilis and the importance of this subunit in the transcriptional regulation of B. subtilis. Here, we established strains and the growth conditions in which the α-subunit of RNAP was replaced with a C-terminally truncated version. Transcriptomic and ChAP-chip analyses revealed that α-CTD deficiency reduced the transcription and RNAP binding of genes related to the utilization of secondary carbon sources, transition state responses, and ribosome synthesis. In E. coli, it is known that α-CTD also contributes to the expression of genes related to the utilization of secondary carbon sources and ribosome synthesis. Our results suggest that the biological importance of α-CTD is conserved in B. subtilis and E. coli, but that its specific roles have diversified between these two bacteria.
Collapse
Affiliation(s)
- Satohiko Murayama
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| | - Shu Ishikawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| | - Onuma Chumsakul
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| | - Naotake Ogasawara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| | - Taku Oshima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916–5, Takayama, Ikoma, Nara 630–0192, Japan
| |
Collapse
|
12
|
Transcriptional regulation and adaptation to a high-fiber environment in Bacillus subtilis HH2 isolated from feces of the giant panda. PLoS One 2015; 10:e0116935. [PMID: 25658435 PMCID: PMC4319723 DOI: 10.1371/journal.pone.0116935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 12/16/2014] [Indexed: 02/07/2023] Open
Abstract
In the giant panda, adaptation to a high-fiber environment is a first step for the adequate functioning of intestinal bacteria, as the high cellulose content of the gut due to the panda's vegetarian appetite results in a harsh environment. As an excellent producer of several enzymes and vitamins, Bacillus subtilis imparts various advantages to animals. In our previous study, we determined that several strains of B. subtilis isolated from pandas exhibited good cellulose decomposition ability, and we hypothesized that this bacterial species can survive in and adapt well to a high-fiber environment. To evaluate this hypothesis, we employed RNA-Seq technology to analyze the differentially expressed genes of the selected strain B. subtilis HH2, which demonstrates significant cellulose hydrolysis of different carbon sources (cellulose and glucose). In addition, we used bioinformatics software and resources to analyze the functions and pathways of differentially expressed genes. Interestingly, comparison of the cellulose and glucose groups revealed that the up-regulated genes were involved in amino acid and lipid metabolism or transmembrane transport, both of which are involved in cellulose utilization. Conversely, the down-regulated genes were involved in non-essential functions for bacterial life, such as toxin and bacteriocin secretion, possibly to conserve energy for environmental adaptation. The results indicate that B. subtilis HH2 triggered a series of adaptive mechanisms at the transcriptional level, which suggests that this bacterium could act as a probiotic for pandas fed a high-fiber diet, despite the fact that cellulose is not a very suitable carbon source for this bacterial species. In this study, we present a model to understand the dynamic organization of and interactions between various functional and regulatory networks for unicellular organisms in a high-fiber environment.
Collapse
|
13
|
Kierul K, Voigt B, Albrecht D, Chen XH, Carvalhais LC, Borriss R. Influence of root exudates on the extracellular proteome of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Microbiology (Reading) 2015; 161:131-147. [DOI: 10.1099/mic.0.083576-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Kinga Kierul
- Institut für Biologie/Bakteriengenetik, Humboldt Universität Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| | - Birgit Voigt
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität, Greifswald, Germany
| | - Dirk Albrecht
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität, Greifswald, Germany
| | - Xiao-Hua Chen
- Institut für Biologie/Bakteriengenetik, Humboldt Universität Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| | - Lilia C. Carvalhais
- Molecular Plant Nutrition, University of Hohenheim, Stuttgart, Germany
- Institut für Biologie/Bakteriengenetik, Humboldt Universität Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| | - Rainer Borriss
- ABiTEP GmbH, Berlin, Germany
- Institut für Biologie/Bakteriengenetik, Humboldt Universität Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| |
Collapse
|
14
|
Overkamp W, Ercan O, Herber M, van Maris AJA, Kleerebezem M, Kuipers OP. Physiological and cell morphology adaptation of Bacillus subtilis at near-zero specific growth rates: a transcriptome analysis. Environ Microbiol 2014; 17:346-63. [PMID: 25367190 DOI: 10.1111/1462-2920.12676] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 10/10/2014] [Accepted: 10/16/2014] [Indexed: 11/27/2022]
Abstract
Nutrient scarcity is a common condition in nature, but the resulting extremely low growth rates (below 0.025 h(-1) ) are an unexplored research area in Bacillus subtilis. To understand microbial life in natural environments, studying the adaptation of B. subtilis to near-zero growth conditions is relevant. To this end, a chemostat modified for culturing an asporogenous B. subtilis sigF mutant strain at extremely low growth rates (also named a retentostat) was set up, and biomass accumulation, culture viability, metabolite production and cell morphology were analysed. During retentostat culturing, the specific growth rate decreased to a minimum of 0.00006 h(-1) , corresponding to a doubling time of 470 days. The energy distribution between growth and maintenance-related processes showed that a state of near-zero growth was reached. Remarkably, a filamentous cell morphology emerged, suggesting that cell separation is impaired under near-zero growth conditions. To evaluate the corresponding molecular adaptations to extremely low specific growth, transcriptome changes were analysed. These revealed that cellular responses to near-zero growth conditions share several similarities with those of cells during the stationary phase of batch growth. However, fundamental differences between these two non-growing states are apparent by their high viability and absence of stationary phase mutagenesis under near-zero growth conditions.
Collapse
Affiliation(s)
- Wout Overkamp
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA, Delft, The Netherlands
| | | | | | | | | | | |
Collapse
|
15
|
Zeigler DR. The Geobacillus paradox: why is a thermophilic bacterial genus so prevalent on a mesophilic planet? Microbiology (Reading) 2014; 160:1-11. [DOI: 10.1099/mic.0.071696-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The genus Geobacillus comprises endospore-forming obligate thermophiles. These bacteria have been isolated from cool soils and even cold ocean sediments in anomalously high numbers, given that the ambient temperatures are significantly below their minimum requirement for growth. Geobacilli are active in environments such as hot plant composts, however, and examination of their genome sequences reveals that they are endowed with a battery of sensors, transporters and enzymes dedicated to hydrolysing plant polysaccharides. Although they appear to be relatively minor members of the plant biomass-degrading microbial community, Geobacillus bacteria have achieved a significant population with a worldwide distribution, probably in large part due to adaptive features of their spores. First, their morphology and resistance properties enable them to be mobilized in the atmosphere and transported long distances. Second, their longevity, which in theory may be extreme, enables them to lie quiescent but viable for long periods of time, accumulating gradually over time to achieve surprisingly high population densities.
Collapse
Affiliation(s)
- Daniel R. Zeigler
- Department of Microbiology, Ohio State University, 484 W 12th Ave, Columbus, OH 43210, USA
| |
Collapse
|
16
|
ManR, a novel Zn(II)2Cys6 transcriptional activator, controls the β-mannan utilization system in Aspergillus oryzae. Fungal Genet Biol 2012; 49:987-95. [DOI: 10.1016/j.fgb.2012.09.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 09/08/2012] [Accepted: 09/10/2012] [Indexed: 11/19/2022]
|
17
|
Yano K, Mien YL, Sadaie Y, Asai K. Bacillus subtilis RNA polymerase incorporates digoxigenin-labeled nucleotide in vitro. J GEN APPL MICROBIOL 2011; 57:153-7. [PMID: 21817827 DOI: 10.2323/jgam.57.153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Koichi Yano
- Area of Biochemistry and Molecular Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama, Saitama 338-8570, Japan
| | | | | | | |
Collapse
|
18
|
Regulon of the N-acetylglucosamine utilization regulator NagR in Bacillus subtilis. J Bacteriol 2011; 193:3525-36. [PMID: 21602348 DOI: 10.1128/jb.00264-11] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
N-Acetylglucosamine (GlcNAc) is the most abundant carbon-nitrogen biocompound on earth and has been shown to be an important source of nutrients for both catabolic and anabolic purposes in Bacillus species. In this work we show that the GntR family regulator YvoA of Bacillus subtilis serves as a negative transcriptional regulator of GlcNAc catabolism gene expression. YvoA represses transcription by binding a 16-bp sequence upstream of nagP encoding the GlcNAc-specific EIIBC component of the sugar phosphotransferase system involved in GlcNAc transport and phosphorylation, as well as another very similar 16-bp sequence upstream of the nagAB-yvoA locus, wherein nagA codes for N-acetylglucosamine-6-phosphate deacetylase and nagB codes for the glucosamine-6-phosphate (GlcN-6-P) deaminase. In vitro experiments demonstrated that GlcN-6-P acts as an inhibitor of YvoA DNA-binding activity, as occurs for its Streptomyces ortholog, DasR. Interestingly, we observed that the expression of nag genes was still activated upon addition of GlcNAc in a ΔyvoA mutant background, suggesting the existence of an auxiliary transcriptional control instance. Initial computational prediction of the YvoA regulon showed a distribution of YvoA binding sites limited to nag genes and therefore suggests renaming YvoA to NagR, for N-acetylglucosamine utilization regulator. Whole-transcriptome studies showed significant repercussions of nagR deletion for several major B. subtilis regulators, probably indirectly due to an excess of the crucial molecules acetate, ammonia, and fructose-6-phosphate, resulting from complete hydrolysis of GlcNAc. We discuss a model deduced from NagR-mediated gene expression, which highlights clear connections with pathways for GlcNAc-containing polymer biosynthesis and adaptation to growth under oxygen limitation.
Collapse
|