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Fang K, Xu Z, Yang L, Cui Q, Du B, Liu H, Wang R, Li P, Su J, Wang J. Biosynthesis of 10-Hydroxy-2-decenoic Acid through a One-Step Whole-Cell Catalysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1190-1202. [PMID: 38175798 DOI: 10.1021/acs.jafc.3c08142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
10-Hydroxy-2-decenoic acid (10-HDA) is an important component of royal jelly, known for its antimicrobial, anti-inflammatory, blood pressure-lowering, and antiradiation effects. Currently, 10-HDA biosynthesis is limited by the substrate selectivity of acyl-coenzyme A dehydrogenase, which restricts the technique to a two-step process. This study aimed to develop an efficient and simplified method for synthesizing 10-HDA. In this study, ACOX from Candida tropicalis 1798, which catalyzes 10-hydroxydecanoyl coenzyme A desaturation for 10-HDA synthesis, was isolated and heterologously coexpressed with FadE, Macs, YdiI, and CYP in Escherichia coli/SK after knocking out FadB, FadJ, and FadR genes. The engineered E. coli/AKS strain achieved a 49.8% conversion of decanoic acid to 10-HDA. CYP expression was improved through ultraviolet mutagenesis and high-throughput screening, increased substrate conversion to 75.6%, and the synthesis of 10-HDA was increased to 0.628 g/L in 10 h. This is the highest conversion rate and product concentration achieved in the shortest time to date. This study provides a simple and efficient method for 10-HDA biosynthesis and offers an effective method for developing strains with high product yields.
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Affiliation(s)
- Ke Fang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Ziting Xu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Lu Yang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Quan Cui
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Bowen Du
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Huijing Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Jing Su
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan 250353, Shandong, Republic of China
- School of Bioengineering, Qilu University of Technology, Jinan 250353, Shandong, Republic of China
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Fang K, Ma J, Wang X, Xu Z, Zhang Z, Li P, Wang R, Wang J, Sun C, Dong Z. Flow-cytometric cell sorting coupled with UV mutagenesis for improving pectin lyase expression. Front Bioeng Biotechnol 2023; 11:1251342. [PMID: 37720319 PMCID: PMC10502208 DOI: 10.3389/fbioe.2023.1251342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction: Alkaline pectin lyase is an important enzyme with a wide range of applications in industrial production, It has been widely used in many important fields such as fruit juice processing and extraction, the dyeing and processing of cotton and linen textiles, degumming plant fibers, environmental industrial wastewater treatment, and pulp and paper production. PGLA-rep4 was previously generated as a modified alkaline pectin lyase with high specific activity at pH 11.0°C and 70°C. However, the pre-constructed high-activity pectin lyase expression strains are still difficult to apply in industrial production due to their limited enzymatic activity. We hope to solve these problems by combining modern breeding techniques with high-throughput equipment to rapidly screen alkaline pectin lyase with higher enzymatic activity and lower cost. Methods: We fused the genes encoding PGLA-rep4 and fluorescent protein egfp using a flexible linker peptide and ligated them into a temperature-sensitive plasmid, pKD46. The constructed screening plasmid pKD46-PGLA-rep4-egfp was then transformed into an expression host and screened via flow-cytometric cell sorting coupled with UV mutagenesis. Results: Following mutagenesis, primary screening, and secondary screening, the high-expression strain, named Escherichia coli BL21/1G3, was obtained. The screening plasmid pKD46-PGLA-rep4-egfp was eliminated, and the original expression plasmid pET28a-PGLA-rep4 was then retransformed into the mutant strains. After induction and fermentation, pectin lyase activity in E. coli BL21/1G3 was significantly increased (1.37-fold relative to that in the parental E. coli BL21/PGLA-rep4 strain, p < 0.001), and the highest activity was 230, 240 U/mL at 144 h. Genome sequencing revealed that genes encoding ribonuclease E (RNase E) and diadenosine tetraphosphatase (ApaH) of E. coli BL21/1G3 were mutated compared to the sequence in the original E. coli BL21 (DE3) strain, which could be associated with increased enzyme expression. Discussion: Our work provides an effective method for the construction of strains expressing pectin lyase at high levels.
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Affiliation(s)
- Ke Fang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Jun Ma
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Xinyu Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Ziting Xu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Ziyang Zhang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Chuying Sun
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Ziyang Dong
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
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Polyribosome-Dependent Clustering of Membrane-Anchored RNA Degradosomes To Form Sites of mRNA Degradation in Escherichia coli. mBio 2021; 12:e0193221. [PMID: 34488454 PMCID: PMC8546579 DOI: 10.1128/mbio.01932-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The essential endoribonuclease RNase E, which is a component of the Escherichia coli multienzyme RNA degradosome, has a global role in RNA processing and degradation. RNase E localizes to the inner cytoplasmic membrane in small, short-lived clusters (puncta). Rifampin, which arrests transcription, inhibits RNase E clustering and increases its rate of diffusion. Here, we show that inhibition of clustering is due to the arrest of transcription using a rifampin-resistant control strain. Two components of the RNA degradosome, the 3′ exoribonuclease polynucleotide phosphorylase (PNPase) and the DEAD box RNA helicase RhlB, colocalize with RNase E in puncta. Clustering of PNPase and RhlB is inhibited by rifampin, and their diffusion rates increase, as evidenced by in vivo photobleaching measurements. Results with rifampin treatment reported here show that RNA degradosome diffusion is constrained by interaction with RNA substrate. Kasugamycin, which arrests translation initiation, inhibits formation of puncta and increases RNA degradosome diffusion rates. Since kasugamycin treatment results in continued synthesis and turnover of ribosome-free mRNA but inhibits polyribosome formation, RNA degradosome clustering is therefore polyribosome dependent. Chloramphenicol, which arrests translation elongation, results in formation of large clusters (foci) of RNA degradosomes that are distinct from puncta. Since chloramphenicol-treated ribosomes are stable, the formation of RNA degradosome foci could be part of a stress response that protects inactive polyribosomes from degradation. Our results strongly suggest that puncta are sites where translationally active polyribosomes are captured by membrane-associated RNA degradosomes. These sites could be part of a scanning process that is an initial step in mRNA degradation.
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Guleria S, Joshi R, Singh D, Kumar S. Identification of host factors limiting the overexpression of recombinant Cu, Zn superoxide dismutase in Escherichia coli. Biotechnol Lett 2020; 42:2389-2401. [DOI: 10.1007/s10529-020-02962-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 07/03/2020] [Indexed: 11/24/2022]
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Bechhofer DH, Deutscher MP. Bacterial ribonucleases and their roles in RNA metabolism. Crit Rev Biochem Mol Biol 2019; 54:242-300. [PMID: 31464530 PMCID: PMC6776250 DOI: 10.1080/10409238.2019.1651816] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent years, there has been a surge of new information about RNases and the roles they play in cell physiology. In this review, a detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Bacillus subtilis, the model Gram-negative and Gram-positive organisms, from which most of our current knowledge has been derived. Information from other organisms is also included, where relevant. In an extensive catalog of the known bacterial RNases, their structure, mechanism of action, physiological roles, genetics, and possible regulation are described. The RNase complement of E. coli and B. subtilis is compared, emphasizing the similarities, but especially the differences, between the two. Included are figures showing the three major RNA metabolic pathways in E. coli and B. subtilis and highlighting specific steps in each of the pathways catalyzed by the different RNases. This compilation of the currently available knowledge about bacterial RNases will be a useful tool for workers in the RNA field and for others interested in learning about this area.
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Affiliation(s)
- David H. Bechhofer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Murray P. Deutscher
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
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Pillon MC, Stanley RE. Nuclease integrated kinase super assemblies (NiKs) and their role in RNA processing. Curr Genet 2017; 64:183-190. [PMID: 28929238 DOI: 10.1007/s00294-017-0749-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 01/24/2023]
Abstract
Here we highlight the Grc3/Las1 complex, an essential RNA processing machine that is well conserved across eukaryotes and required for processing the pre-ribosomal RNA (pre-rRNA). Las1 is an endoribonuclease that cleaves the pre-rRNA while Grc3 is a polynucleotide kinase that phosphorylates the Las1-cleaved RNA product. Recently we showed that Grc3 and Las1 assemble into a higher-order complex composed of a dimer of Grc3/Las1 heterodimers that is required for nuclease and kinase activity. Unexpectedly, we found that the Grc3/Las1 complex draws numerous parallels with two other eukaryotic nucleases, Ire1 and RNase L. In this perspective we explore the similarities and differences between this family of nuclease integrated kinase super assemblies (NiKs) and their distinct roles in RNA cleavage.
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Affiliation(s)
- Monica C Pillon
- Signal Transduction Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
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Searle NE, Pillus L. Critical genomic regulation mediated by Enhancer of Polycomb. Curr Genet 2017; 64:147-154. [PMID: 28884217 DOI: 10.1007/s00294-017-0742-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 01/28/2023]
Abstract
Enhancer of Polycomb (EPC) was first identified for its contributions to development in Drosophila and was soon-thereafter purified as a subunit of the NuA4/TIP60 acetyltransferase complex. Since then, EPC has often been left in the shadows as an essential, yet non-catalytic subunit of NuA4/TIP60; however, its deep conservation and disease association make clear that it warrants additional attention. In fact, recent studies in yeast demonstrated that its Enhancer of Polycomb, Epl1, was just as important for gene expression and acetylation as is the catalytic subunit of NuA4. Despite its conservation, studies of EPC have often remained siloed between organisms. Here, our goal is to provide a cohesive view of the current state of the EPC literature as it stands among the major model organisms in which it has been studied. EPC is involved in multiple processes, beginning with its cardinal role in regulating global and targeted histone acetylation. EPC also frequently serves as an important interaction partner in these basic cellular functions, as well as in multicellular development, such as in hematopoiesis and skeletal muscle differentiation, and in human disease. Taken together, a unifying theme from these studies highlights EPC as a critical genomic regulator.
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Affiliation(s)
- Naomi E Searle
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, UC San Diego Moores Cancer Center, 9500 Gilman Drive, La Jolla, CA, 92093-0347, USA.,UC San Diego Biomedical Sciences, La Jolla, CA, 92093-0685, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, UC San Diego Moores Cancer Center, 9500 Gilman Drive, La Jolla, CA, 92093-0347, USA.
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