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Chen L, Wang C, Su J. Understanding the Effect of Different Glucose Concentrations in the Oligotrophic Bacterium Bacillus subtilis BS-G1 through Transcriptomics Analysis. Microorganisms 2023; 11:2401. [PMID: 37894061 PMCID: PMC10609351 DOI: 10.3390/microorganisms11102401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Glucose is an important carbon source for microbial growth, and its content in infertile soils is essential for the growth of bacteria. Since the mechanism of oligotrophic bacterium adaptation in barren soils is unclear, this research employed RNA-seq technology to examine the impact of glucose concentration on the oligotrophic bacterium B. subtilis BS-G1 in soil affected by desertification. A global transcriptome analysis (RNA-Seq) revealed that the significantly differentially expressed genes (DEGs) histidine metabolism, glutamate synthesis, the HIF-1 signaling pathway, sporulation, and the TCA cycle pathway of B. subtilis BS-G1 were significantly enriched with a 0.015 g/L glucose concentration (L group), compared to a 10 g/L glucose concentration (H group). The DEGs amino acid system, two-component system, metal ion transport, and nitrogen metabolism system of B. subtilis BS-G1 were significantly enriched in the 5 g/L glucose concentration (M group), compared with the H group. In addition, the present study identified the regulation pattern and key genes under a low-glucose environment (7 mRNAs and 16 sRNAs). This study primarily investigates the variances in the regulatory pathways of the oligotrophic B. subtilis BS-G1, which holds substantial importance in comprehending the mechanism underlying the limited sugar tolerance of oligotrophic bacteria.
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Affiliation(s)
- Liping Chen
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Chenglong Wang
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
| | - Jianyu Su
- Key Laboratory of Ministry of Education for Protection and Utilization of Special Biological Resources, School of Life Sciences, Ningxia University, Yinchuan 750021, China
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Tenea GN. Metabiotics Signature through Genome Sequencing and In Vitro Inhibitory Assessment of a Novel Lactococcus lactis Strain UTNCys6-1 Isolated from Amazonian Camu-Camu Fruits. Int J Mol Sci 2023; 24:ijms24076127. [PMID: 37047101 PMCID: PMC10094308 DOI: 10.3390/ijms24076127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/12/2023] [Accepted: 03/18/2023] [Indexed: 03/29/2023] Open
Abstract
Metabiotics are the structural components of probiotic bacteria, functional metabolites, and/or signaling molecules with numerous beneficial properties. A novel Lactococcus lactis strain, UTNCys6-1, was isolated from wild Amazonian camu-camu fruits (Myrciaria dubia), and various functional metabolites with antibacterial capacity were found. The genome size is 2,226,248 base pairs, and it contains 2248 genes, 2191 protein-coding genes (CDSs), 50 tRNAs, 6 rRNAs, 1 16S rRNA, 1 23S rRNA, and 1 tmRNA. The average GC content is 34.88%. In total, 2148 proteins have been mapped to the EggNOG database. The specific annotation consisted of four incomplete prophage regions, one CRISPR-Cas array, six genomic islands (GIs), four insertion sequences (ISs), and four regions of interest (AOI regions) spanning three classes of bacteriocins (enterolysin_A, nisin_Z, and sactipeptides). Based on pangenome analysis, there were 6932 gene clusters, of which 751 (core genes) were commonly observed within the 11 lactococcal strains. Among them, 3883 were sample-specific genes (cloud genes) and 2298 were shell genes, indicating high genetic diversity. A sucrose transporter of the SemiSWEET family (PTS system: phosphoenolpyruvate-dependent transport system) was detected in the genome of UTNCys6-1 but not the other 11 lactococcal strains. In addition, the metabolic profile, antimicrobial susceptibility, and inhibitory activity of both protein–peptide extract (PPE) and exopolysaccharides (EPSs) against several foodborne pathogens were assessed in vitro. Furthermore, UTNCys6-1 was predicted to be a non-human pathogen that was unable to tolerate all tested antibiotics except gentamicin; metabolized several substrates; and lacks virulence factors (VFs), genes related to the production of biogenic amines, and acquired antibiotic resistance genes (ARGs). Overall, this study highlighted the potential of this strain for producing bioactive metabolites (PPE and EPSs) for agri-food and pharmaceutical industry use.
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Papadopoulou E, Rodriguez de Evgrafov MC, Kalea A, Tsapekos P, Angelidaki I. Adaptive laboratory evolution to hypersaline conditions of lactic acid bacteria isolated from seaweed. N Biotechnol 2023; 75:21-30. [PMID: 36870677 DOI: 10.1016/j.nbt.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/20/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Seaweed biomass has been proposed as a promising alternative carbon source for fermentation processes using microbial factories. However, the high salinity content of seaweed biomass is a limiting factor in large scale fermentation processes. To address this shortcoming, three bacterial species (Pediococcus pentosaceus, Lactobacillus plantarum, and Enterococcus faecium) were isolated from seaweed biomass and evolved to increasing concentrations of NaCl. Following the evolution period, P. pentosaceus reached a plateau at the initial NaCl concentration, whereas L. plantarum, and E. faecium showed a 1.29 and 1.75-fold increase in their salt tolerance, respectively. The impact that salt evolution had on lactic acid production using hypersaline seaweed hydrolysate was investigated. Salinity evolved L. plantarum produced 1.18-fold more lactic acid than the wild type, and salinity evolved E. faecium was able to produce lactic acid, while the wild type could not. No differences in lactic acid production were observed between the P. pentosaceus salinity evolved and wild type strains. Evolved lineages were analyzed for the molecular mechanisms underlying the observed phenotypes. Mutations were observed in genes affecting the ion balance in the cell, the composition of the cell membrane and proteins acting as regulators. This study demonstrates that bacterial isolates from saline niches are promising microbial factories for the fermentation of saline substrates, without the requirement of previous desalination steps, while preserving high final product yields.
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Affiliation(s)
- Eleftheria Papadopoulou
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | | | - Argyro Kalea
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Panagiotis Tsapekos
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
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Qiu Y, Qiu Z, Xia J, Liu X, Zhang H, Yang Y, Hou W, Li X, He J. Co-expression of Xylose Transporter and Fructose-Bisphosphate Aldolase Enhances the Utilization of Xylose by Lactococcus lactis IO-1. Appl Biochem Biotechnol 2023; 195:816-831. [PMID: 36205844 DOI: 10.1007/s12010-022-04168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 01/24/2023]
Abstract
The raw material cost of lactic acid fermentation accounts for the main part of the production cost, and this necessitates the exploration of the efficient use of cheap raw materials in lactic acid production. We compared the outcomes of the homologous expressions of xylose transporters (xylFGH, xylE, araE, and xylT), 6-phosphofructokinase (pfkA), fructose-bisphosphate aldolase (fbaA), and their co-expression in Lactococcus lactis IO-1 on lactic acid production using xylose as the raw material. We found that the production rate of lactic acid on xylose fermentation by L. lactis IO-1 overexpressing fbaA was the highest (14.42%). Among the xylose transporters investigated, XylT had the strongest xylose transport capacity in L. lactis IO-1, with an increase in the lactic acid production rate by 10.38%. The genes near the overexpression of fbaA or xylT in the metabolic pathway were more upregulated than the distant genes. The co-expression of fbaA and xylT increased the production rate of lactic acid by 27.84% on xylose fermentation by L. lactis IO-1. This work presents a novel strategy for the simultaneous enhancement of the expression of important genes at the beginning and midway of the xylose metabolic pathway of L. lactis IO-1, which could greatly improve the target production.
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Affiliation(s)
- Yejuan Qiu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Zhongyang Qiu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Jun Xia
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Xiaoyan Liu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Hanwen Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Yuxiang Yang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Wenyi Hou
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Xiangqian Li
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China.
| | - Jianlong He
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China.
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Okoye CO, Dong K, Wang Y, Gao L, Li X, Wu Y, Jiang J. Comparative genomics reveals the organic acid biosynthesis metabolic pathways among five lactic acid bacterial species isolated from fermented vegetables. N Biotechnol 2022; 70:73-83. [PMID: 35525431 DOI: 10.1016/j.nbt.2022.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/28/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022]
Abstract
Lactic acid bacteria (LAB) comprise a widespread bacterial group, inhabiting the niches of fermented vegetables and capable of producing beneficial organic acids. In the present study, several bioinformatics approaches were used to perform whole-genome sequencing and comparative genomics of five LAB species, Lactobacillus plantarum PC1-1, Pediococcus pentosaceus PC2-1(F2), Weissella hellenica PC1A, Lactobacillus buchneri PC-C1, and Enterococcus sp. YC2-6, to enhance understanding of their different genetic functionalities and organic acid biosynthesis. The results revealed major carbohydrate-active enzymes, putative operons and unique mobile genetic elements, including plasmids, resistance genes, insertion sequences and composite transposons involved in organic acid biosynthesis. The metabolic pathways of organic acid biosynthesis emphasize the key genes encoding specific enzymes required for organic acid metabolism. The five genomes were found to contain various regions of secondary metabolite biosynthetic gene clusters, including the type III polyketide synthases (T3PKS) enriched with unique genes encoding a hydroxymethylglutaryl-CoA synthase, capable of exhibiting specific antimicrobial activity with biopreservative potential, and a cyclic AMP receptor protein (CPR) transcription factor acting as a glucose sensor in organic acid biosynthesis. This could enable the organisms to prevail in the fermentation process, suggesting potential industrial applications.
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Affiliation(s)
- Charles Obinwanne Okoye
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria
| | - Ke Dong
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yongli Wang
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Lu Gao
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xia Li
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yanfang Wu
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jianxiong Jiang
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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Bandera AM, Bartho J, Lammens K, Drexler DJ, Kleinschwärzer J, Hopfner KP, Witte G. BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture. Nucleic Acids Res 2021; 49:10166-10177. [PMID: 34432045 PMCID: PMC8517857 DOI: 10.1093/nar/gkab736] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/27/2021] [Accepted: 08/12/2021] [Indexed: 12/18/2022] Open
Abstract
The cyclic dinucleotide second messenger c-di-AMP is a major player in regulation of potassium homeostasis and osmolyte transport in a variety of bacteria. Along with various direct interactions with proteins such as potassium channels, the second messenger also specifically binds to transcription factors, thereby altering the processes in the cell on the transcriptional level. We here describe the structural and biochemical characterization of BusR from the human pathogen Streptococcus agalactiae. BusR is a member of a yet structurally uncharacterized subfamily of the GntR family of transcription factors that downregulates transcription of the genes for the BusA (OpuA) glycine-betaine transporter upon c-di-AMP binding. We report crystal structures of full-length BusR, its apo and c-di-AMP bound effector domain, as well as cryo-EM structures of BusR bound to its operator DNA. Our structural data, supported by biochemical and biophysical data, reveal that BusR utilizes a unique domain assembly with a tetrameric coiled-coil in between the binding platforms, serving as a molecular ruler to specifically recognize a 22 bp separated bipartite binding motif. Binding of c-di-AMP to BusR induces a shift in equilibrium from an inactivated towards an activated state that allows BusR to bind the target DNA, leading to transcriptional repression.
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Affiliation(s)
- Adrian M Bandera
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Joseph Bartho
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Katja Lammens
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - David Jan Drexler
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Jasmin Kleinschwärzer
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Karl-Peter Hopfner
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Gregor Witte
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
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Ardalani O, Motamedian E, Hamedi J. Reconstruction and validation of genome-scale metabolic model of L. lactis subsp. lactis NCDO 2118 and in silico analysis for succinate and Gamma-aminobutyric acid overproduction. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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