Bacterial Engineering and Metabolism Regulation

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: 30 April 2024 | Viewed by 9043

Special Issue Editors


E-Mail Website
Guest Editor
State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
Interests: metabolic engineering; biobased materials and chemicals; gene expression regulation; bacterial stress response

E-Mail Website
Guest Editor
State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
Interests: metabolic engineering; genome editing; bioinformatics; enzyme engineering

Special Issue Information

Dear Colleagues,

Bacteria are the most widely distributed living organisms on the planet with various and complex metabolic mechanisms which play vital roles in the environment, human health, food, industry, and many other areas. Various techniques have been developed for the regulation of the bacterial metabolism and the exploration of its mechanism, including transcriptomic methods, proteomics, metabolomics, adaptive evolution, gene editing, and so on. In recent decades, many bacteria have been engineered for a chemical production, agricultural wastes utilization, ecological regulation, environmental protection, and even disease treatments. Although great progress has been made, our knowledge regarding the regulation of the metabolism is still insufficient, hindering further bacteria engineering and the expansion of their application.

The aim of this Special Issue of Microorganisms is to present a collection of articles related to regulation of the bacterial metabolism and bacterial engineering (both basic and applied research). As a Guest Editor of this Special Issue, I invite you to submit research articles, review articles, and short communications. The topics of interest for this Special Issue include, but are not limited to, the following: bacteria metabolic engineering, bacteria regulation mechanisms, transcription factor, gene editing, strain construction and optimization, the production of high-value compounds, and new methods or techniques for bacteria engineering and regulation exploration.

Prof. Dr. Guang Zhao
Dr. Jichao Wang
Guest Editors

Manuscript Submission Information

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Keywords

  • metabolism regulation
  • regulatory mechanism
  • transcriptional regulation
  • transcription factor
  • post-translational modifications
  • metabolic engineering
  • genome editing
  • chassis cells
  • strain optimization

Published Papers (6 papers)

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Research

25 pages, 1989 KiB  
Article
Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species
by Heba Farookhi and Xuhua Xia
Microorganisms 2024, 12(4), 768; https://doi.org/10.3390/microorganisms12040768 - 10 Apr 2024
Viewed by 530
Abstract
Different bacterial species have dramatically different generation times, from 20–30 min in Escherichia coli to about two weeks in Mycobacterium leprae. The translation machinery in a cell needs to synthesize all proteins for a new cell in each generation. The three subprocesses [...] Read more.
Different bacterial species have dramatically different generation times, from 20–30 min in Escherichia coli to about two weeks in Mycobacterium leprae. The translation machinery in a cell needs to synthesize all proteins for a new cell in each generation. The three subprocesses of translation, i.e., initiation, elongation, and termination, are expected to be under stronger selection pressure to optimize in short-generation bacteria (SGB) such as Vibrio natriegens than in the long-generation Mycobacterium leprae. The initiation efficiency depends on the start codon decoded by the initiation tRNA, the optimal Shine–Dalgarno (SD) decoded by the anti-SD (aSD) sequence on small subunit rRNA, and the secondary structure that may embed the initiation signals and prevent them from being decoded. The elongation efficiency depends on the tRNA pool and codon usage. The termination efficiency in bacteria depends mainly on the nature of the stop codon and the nucleotide immediately downstream of the stop codon. By contrasting SGB with long-generation bacteria (LGB), we predict (1) SGB to have more ribosome RNA operons to produce ribosomes, and more tRNA genes for carrying amino acids to ribosomes, (2) SGB to have a higher percentage of genes using AUG as the start codon and UAA as the stop codon than LGB, (3) SGB to exhibit better codon and anticodon adaptation than LGB, and (4) SGB to have a weaker secondary structure near the translation initiation signals than LGB. These differences between SGB and LGB should be more pronounced in highly expressed genes than the rest of the genes. We present empirical evidence in support of these predictions. Full article
(This article belongs to the Special Issue Bacterial Engineering and Metabolism Regulation)
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15 pages, 4449 KiB  
Article
Effects of Environmental Stresses on Synthesis of 2-Phenylethanol and IAA by Enterobacter sp. CGMCC 5087
by Ke Li, Senbiao Fang, Xiao Zhang, Xiaodi Wei, Pingle Wu, Rong Zheng, Lijuan Liu and Haibo Zhang
Microorganisms 2024, 12(4), 663; https://doi.org/10.3390/microorganisms12040663 - 26 Mar 2024
Viewed by 482
Abstract
2-Phenylethanol (2-PE) and indole-3-acetic acid (IAA) are important secondary metabolites produced by microorganisms, and their production are closely linked to the growth state of microorganisms and environmental factors. Enterobacter CGMCC 5087 can produce both 2-PE and IAA depending on α-ketoacid decarboxylase KDC4427. This [...] Read more.
2-Phenylethanol (2-PE) and indole-3-acetic acid (IAA) are important secondary metabolites produced by microorganisms, and their production are closely linked to the growth state of microorganisms and environmental factors. Enterobacter CGMCC 5087 can produce both 2-PE and IAA depending on α-ketoacid decarboxylase KDC4427. This study aimed to investigate the effects of different environment factors including osmotic pressure, temperature, and pH on the synthesis of 2-PE and IAA in Enterobacter sp. CGMCC 5087. The bacteria exhibited an enhanced capacity for 2-PE synthesis while not affecting IAA synthesis under 5% NaCl and pH 4.5 stress conditions. In an environment with pH 9.5, the synthesis capacity of 2-PE remained unchanged while the synthesis capacity of IAA decreased. The synthesis ability of 2-PE was enhanced with an increase in temperature within the range of 25 °C to 37 °C, while the synthesis capacity of IAA was not affected significantly. Additionally, the expression of KDC4427 varied under stress conditions. Under 5% NaCl stress and decreased temperature, expression of the KDC4427 gene was increased. However, altering pH did not result in significant differences in gene expression levels, while elevated temperature caused a decrease in gene expression. Furthermore, molecular docking and molecular dynamics simulations suggested that these conditions may induce fluctuation in the geometry shape of binding cavity, binding energy, and especially the dαC-C- value, which played key roles in affecting the enzyme activity. These results provide insights and strategies for the synthesis of metabolic products 2-PE and IAA in bacterial fermentation, even under unfavorable conditions. Full article
(This article belongs to the Special Issue Bacterial Engineering and Metabolism Regulation)
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22 pages, 7025 KiB  
Article
Time-Course Transcriptome Analysis of Bacillus subtilis DB104 during Growth
by Ji-Su Jun, Hyang-Eun Jeong, Su-Yeong Moon, Se-Hee Shin and Kwang-Won Hong
Microorganisms 2023, 11(8), 1928; https://doi.org/10.3390/microorganisms11081928 - 28 Jul 2023
Cited by 1 | Viewed by 1488
Abstract
Bacillus subtilis DB104, an extracellular protease-deficient derivative of B. subtilis 168, is widely used for recombinant protein expression. An understanding of the changes in gene expression during growth is essential for the commercial use of bacterial strains. Transcriptome and proteome analyses are ideal [...] Read more.
Bacillus subtilis DB104, an extracellular protease-deficient derivative of B. subtilis 168, is widely used for recombinant protein expression. An understanding of the changes in gene expression during growth is essential for the commercial use of bacterial strains. Transcriptome and proteome analyses are ideal methods to study the genomic response of microorganisms. In this study, transcriptome analysis was performed to monitor changes in the gene expression level of B. subtilis DB104 while growing on a complete medium. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, K-mean cluster analysis, gene ontology (GO) enrichment analysis, and the function of sigma factors were used to divide 2122 differentially expressed genes (DEGs) into 10 clusters and identified gene functions according to expression patterns. The results of KEGG pathway analysis indicated that ABC transporter is down-regulated during exponential growth and metabolic changes occur at the transition point where sporulation starts. At this point, several stress response genes were also turned on. The genes involved in the lipid catabolic process were up-regulated briefly at 15 h as an outcome of the programmed cell death that postpones sporulation. The results suggest that changes in the gene expression of B. subtilis DB104 were dependent on the initiation of sporulation. However, the expression timing of the spore coat gene was only affected by the relevant sigma factor. This study can help to understand gene expression and regulatory mechanisms in B. subtilis species by providing an overall view of transcriptional changes during the growth of B. subtilis DB104. Full article
(This article belongs to the Special Issue Bacterial Engineering and Metabolism Regulation)
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10 pages, 1538 KiB  
Article
Extracellular Expression of Feruloyl Esterase and Xylanase in Escherichia coli for Ferulic Acid Production from Agricultural Residues
by Jiaxin Lan, Shujie Ji, Chuanjia Yang, Guolin Cai, Jian Lu and Xiaomin Li
Microorganisms 2023, 11(8), 1869; https://doi.org/10.3390/microorganisms11081869 - 25 Jul 2023
Cited by 1 | Viewed by 871
Abstract
There is still a large amount of ferulic acid (FA), an outstanding antioxidant, present in agricultural residues. Enzymatic hydrolysis has been regarded as the most effective way to release FA. This present study therefore selected feruloyl esterase (FAE) and xylanase (XYN) from the [...] Read more.
There is still a large amount of ferulic acid (FA), an outstanding antioxidant, present in agricultural residues. Enzymatic hydrolysis has been regarded as the most effective way to release FA. This present study therefore selected feruloyl esterase (FAE) and xylanase (XYN) from the metagenomes of a cow rumen and a camel rumen, respectively, for their recombinant expression in Escherichia coli BL21 and further application in releasing FA. After screening the candidate signal peptides, the optimal one for each enzyme, which were selected as SP1 and SP4, respectively, was integrated into the vectors pET22b(+) and pETDuet-1. Among the generated E. coli strains SP1-F, SP4-X, and SP1-F-SP4-X that could express extracellular enzymes either separately or simultaneously, the latter one performed the best in relation to degrading the biomass and releasing FA. Under the optimized culture and induction conditions, the strain SP1-F-SP4-X released 90% of FA from 10% of de-starched wheat bran and produced 314.1 mg/L FA, which was deemed to be the highest obtained value to the best of our knowledge. This result could pave a way for the re-utilization of agricultural residues and enhancing their add-value. Full article
(This article belongs to the Special Issue Bacterial Engineering and Metabolism Regulation)
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14 pages, 4192 KiB  
Article
Tryptophanase Expressed by Salmonella Halts Breast Cancer Cell Growth In Vitro and Inhibits Production of Immunosuppressive Kynurenine
by Eljoie Anice Cada Hababag, Allea Cauilan, David Quintero and David Bermudes
Microorganisms 2023, 11(5), 1355; https://doi.org/10.3390/microorganisms11051355 - 22 May 2023
Viewed by 1751
Abstract
Tryptophan is an essential amino acid required for tumor cell growth and is also the precursor to kynurenine, an immunosuppressive molecule that plays a role in limiting anticancer immunity. Tryptophanase (TNase) is an enzyme expressed by different bacterial species that converts tryptophan into [...] Read more.
Tryptophan is an essential amino acid required for tumor cell growth and is also the precursor to kynurenine, an immunosuppressive molecule that plays a role in limiting anticancer immunity. Tryptophanase (TNase) is an enzyme expressed by different bacterial species that converts tryptophan into indole, pyruvate and ammonia, but is absent in the Salmonella strain VNP20009 that has been used as a therapeutic delivery vector. We cloned the Escherichia coli TNase operon tnaCAB into the VNP20009 (VNP20009-tnaCAB), and were able to detect linear production of indole over time, using Kovács reagent. In order to conduct further experiments using the whole bacteria, we added the antibiotic gentamicin to stop bacterial replication. Using a fixed number of bacteria, we found that there was no significant effect of gentamicin on stationary phase VNP20009-tnaCAB upon their ability to convert tryptophan to indole over time. We developed a procedure to extract indole from media while retaining tryptophan, and were able to measure tryptophan spectrophotometrically after exposure to gentamicin-inactivated whole bacterial cells. Using the tryptophan concentration equivalent to that present in DMEM cell culture media, a fixed number of bacteria were able to deplete 93.9% of the tryptophan in the culture media in 4 h. In VNP20009-tnaCAB depleted tissue culture media, MDA-MB-468 triple negative breast cancer cells were unable to divide, while those treated with media exposed only to VNP20009 continued cell division. Re-addition of tryptophan to conditioned culture media restored tumor cell growth. Treatment of tumor cells with molar equivalents of the TNase products indole, pyruvate and ammonia only caused a slight increase in tumor cell growth. Using an ELISA assay, we confirmed that TNase depletion of tryptophan also limits the production of immunosuppressive kynurenine in IFNγ-stimulated MDA-MB-468 cancer cells. Our results demonstrate that Salmonella VNP20009 expressing TNase has improved potential to stop tumor cell growth and reverse immunosuppression. Full article
(This article belongs to the Special Issue Bacterial Engineering and Metabolism Regulation)
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14 pages, 3892 KiB  
Article
Genetic Engineering of Klebsiella pneumoniae ATCC 25955 for Bioconjugate Vaccine Applications
by Yan Liu, Shulei Li, Yan Guo, Xin Li, Li Zhu, Hengliang Wang, Jun Wu and Chao Pan
Microorganisms 2023, 11(5), 1321; https://doi.org/10.3390/microorganisms11051321 - 17 May 2023
Cited by 1 | Viewed by 1654
Abstract
Vaccination is considered the most effective means to fight against the multidrug-resistant strains of Klebsiella pneumoniae. In recent years, a potential protein glycan coupling technology has been extensively used in the production of bioconjugated vaccines. Here, a series of glycoengineering strains derived [...] Read more.
Vaccination is considered the most effective means to fight against the multidrug-resistant strains of Klebsiella pneumoniae. In recent years, a potential protein glycan coupling technology has been extensively used in the production of bioconjugated vaccines. Here, a series of glycoengineering strains derived from K. pneumoniae ATCC 25955 were designed for protein glycan coupling technology. The capsule polysaccharide biosynthesis gene cluster and the O-antigen ligase gene waaL were deleted via the CRISPR/Cas9 system to further weaken the virulence of host stains and block the unwanted endogenous glycan synthesis. Particularly, the SpyCatcher protein in the efficient protein covalent ligation system (SpyTag/SpyCatcher) was selected as the carrier protein to load the bacterial antigenic polysaccharides (O1 serotype), which could covalently bind to SpyTag-functionalized nanoparticles AP205 to form nanovaccines. Furthermore, two genes (wbbY and wbbZ) located in the O-antigen biosynthesis gene cluster were knocked out to change the O1 serotype of the engineered strain into the O2 serotype. Both KPO1-SC and KPO2-SC glycoproteins were successfully obtained as expected using our glycoengineering strains. Our work provides new insights into the design of nontraditional bacterial chassis for bioconjugate nanovaccines against infectious diseases. Full article
(This article belongs to the Special Issue Bacterial Engineering and Metabolism Regulation)
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