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Lamba R, Salam A, Anjum F, Yadav A, Garg R, Kaushik K, Sharma S, Nandi CK. NIR-emissive carbon nanodots as a tool to mark ribosomal RNA and nucleolus components using super-resolution microscopy. NANOSCALE 2024. [PMID: 38864270 DOI: 10.1039/d4nr01569j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Ribosomal RNA (rRNA) plays a key role in protein synthesis and ribosomal biogenesis. The exclusively used commercial dye for RNA staining is SYTO RNASelect, which works in fixed cells only. To overcome this constraint, we synthesized NIR-emissive, highly photostable, and biocompatible carbon nanodots (CNDs) as a fluorescent biomarker for rRNA. The synthesized CNDs could stain rRNA in both live and fixed cells. We were able to visualize rRNA at different sites in eukaryotic cells using super-resolution microscopy (SRM). The CNDs localized rRNA in the dense fibrillar components (DFCs) of the nucleolus, nuclear membrane, and rough endoplasmic reticulum (RER). The super-resolved hollow ring-structured DFC with an FWHM of 140 nm, nuclear membrane with an FWHM of 120 nm, and ER with an FWHM of 115 nm were observed. We further found a marked contrast between the pre-RNA synthesized in cancer cells and normal cells. We believe that these CNDs have great potential in rRNA imaging and comprehending the complex relationships between rRNA dynamics and basic biological processes, disease development, or drug interactions.
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Affiliation(s)
- Rohan Lamba
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
| | - Abdul Salam
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
| | - Farhan Anjum
- School of Biological Sciences and Bioengineering, Indian Institute of Technology Mandi, H.P.-175075, India
| | - Aditya Yadav
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
| | - Richa Garg
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
| | - Kush Kaushik
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
| | - Shagun Sharma
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
| | - Chayan Kanti Nandi
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
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Schmidt M, Lee N, Zhan C, Roberts JB, Nava AA, Keiser LS, Vilchez AA, Chen Y, Petzold CJ, Haushalter RW, Blank LM, Keasling JD. Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies. ACS Synth Biol 2023; 12:3366-3380. [PMID: 37851920 PMCID: PMC10661030 DOI: 10.1021/acssynbio.3c00367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Indexed: 10/20/2023]
Abstract
Type I polyketide synthases (T1PKSs) hold enormous potential as a rational production platform for the biosynthesis of specialty chemicals. However, despite great progress in this field, the heterologous expression of PKSs remains a major challenge. One of the first measures to improve heterologous gene expression can be codon optimization. Although controversial, choosing the wrong codon optimization strategy can have detrimental effects on the protein and product levels. In this study, we analyzed 11 different codon variants of an engineered T1PKS and investigated in a systematic approach their influence on heterologous expression in Corynebacterium glutamicum, Escherichia coli, and Pseudomonas putida. Our best performing codon variants exhibited a minimum 50-fold increase in PKS protein levels, which also enabled the production of an unnatural polyketide in each of these hosts. Furthermore, we developed a free online tool (https://basebuddy.lbl.gov) that offers transparent and highly customizable codon optimization with up-to-date codon usage tables. In this work, we not only highlight the significance of codon optimization but also establish the groundwork for the high-throughput assembly and characterization of PKS pathways in alternative hosts.
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Affiliation(s)
- Matthias Schmidt
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52062 Aachen, Germany
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Namil Lee
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Chunjun Zhan
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jacob B. Roberts
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint
Program in Bioengineering, University of
California, Berkeley, California 94720, United States
| | - Alberto A. Nava
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Leah S. Keiser
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Aaron A. Vilchez
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Yan Chen
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J. Petzold
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Robert W. Haushalter
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lars M. Blank
- Institute
of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52062 Aachen, Germany
| | - Jay D. Keasling
- Joint
BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems & Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint
Program in Bioengineering, University of
California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Center
for Synthetic Biochemistry, Institute for
Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen 518071, China
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Xu X, Ye X, Zhu M, Zhang Q, Li X, Yan J. FtMt reduces oxidative stress-induced trophoblast cell dysfunction via the HIF-1α/VEGF signaling pathway. BMC Pregnancy Childbirth 2023; 23:131. [PMID: 36859279 PMCID: PMC9976428 DOI: 10.1186/s12884-023-05448-1] [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: 11/18/2022] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Preeclampsia (PE) is a complication of pregnancy that causes long-term adverse outcomes for the mother and fetus and may even lead to death. Oxidative stress caused by the imbalance of oxidants and antioxidants in the placenta has been considered as one of the key mechanisms of preeclampsia (together with inflammation, etc.), in which the placental mitochondria play an important role. The expression of hypoxia-inducible factor-1 (HIF-1α) and vascular endothelial growth factor (VEGF) is known to be increased in patients with PE. Mitochondrial ferritin (FtMt) is known to protect the mitochondria from oxidative stress, although its specific role in PE remains unclear. METHODS We used qRT-PCR and western blotting to detect the expression levels of FtMt, HIF-1α, and VEGF in placental tissues from patients with PE. Human chorionic trophoblast cells were also administered with hypoxia treatment, followed by the detection of cell proliferation, invasion and angiogenic capacity by CCK8, Transwell, and endothelial cell angiogenesis assays; we also detected the expression of HIF-1α and VEGF in these cells. Finally, overexpression or inhibitory FtMt lentiviral vectors, along with negative control vectors, were constructed and transfected into hypoxia-treated human chorionic trophoblast cells; this was followed by analyses of cell function. RESULTS The expression levels of FtMt, HIF-1α and VEGF in the PE group were higher than those in the control group (P < 0.05). Following hypoxia, there was an increase in the expression levels of HIF-1α and VEGF protein in trophoblast cells. There was also an increase in invasion ability and vascular formation ability along with a reduction in cell proliferation ability. These effects were reversed by transfecting cells with the knockout FtMt lentivirus vector. The differences were statistically significant. CONCLUSION Analyses showed that FtMt plays a key role in the vascular regulation of PE trophoblast cells after hypoxia possibly acting via the HIF-1α/VEGF signaling pathway. These results provide us an enhanced understanding of the pathogenesis of PE and suggest that the HIF-1α/VEGF signaling pathway represents a new target for the treatment of PE.
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Affiliation(s)
- Xia Xu
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Xu Ye
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Mengwei Zhu
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Qiuyu Zhang
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Xiuli Li
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, Fujian, China
| | - Jianying Yan
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, Fujian, China.
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Ting WW, Yu JY, Lin YC, Ng IS. Enhanced recombinant carbonic anhydrase in T7RNAP-equipped Escherichia coli W3110 for carbon capture storage and utilization (CCSU). BIORESOURCE TECHNOLOGY 2022; 363:128010. [PMID: 36167176 DOI: 10.1016/j.biortech.2022.128010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Sulfurihydrogenibium yellowstonense carbonic anhydrase (SyCA) is a well-known thermophilic CA for carbon mineralization. To broaden the applications of SyCA, the activity of SyCA was improved through stepwise engineering and in different cultural conditions, as well as extended to co-expression with other enzymes. The engineered W3110 strains with 4 different T7 RNA polymerase levels were employed for SyCA production. As a result, the best strain WT7L cultured in modified M9 medium with temperature shifted from 37 to 30 °C after induction increased SyCA activity to 9122 U/mL. The SyCA whole-cell biocatalyst was successfully applied for carbon capture and storage (CCS) of CaCO3. Furthermore, SyCA was applied for low-carbon footprint synthesis of 5-aminolevulinic acid (5-ALA) and cadaverine (DAP) by coupling with ALA synthetase (ALAS) and lysine decarboxylase (CadA), suppressing CO2 release to -6.1 g-CO2/g-ALA and -2.53 g-CO2/g-DAP, respectively. Harnessing a highly active SyCA offers a complete strategy for CCSU in a green process.
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Affiliation(s)
- Wan-Wen Ting
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Jie-Yao Yu
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yu-Chieh Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
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