1
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Alejo JL, Girodat D, Hammerling MJ, Willi JA, Jewett MC, Engelhart AE, Adamala KP. Alternate conformational trajectories in ribosome translocation. PLoS Comput Biol 2024; 20:e1012319. [PMID: 39141679 PMCID: PMC11346969 DOI: 10.1371/journal.pcbi.1012319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 08/26/2024] [Accepted: 07/12/2024] [Indexed: 08/16/2024] Open
Abstract
Translocation in protein synthesis entails the efficient and accurate movement of the mRNA-[tRNA]2 substrate through the ribosome after peptide bond formation. An essential conformational change during this process is the swiveling of the small subunit head domain about two rRNA 'hinge' elements. Using iterative selection and molecular dynamics simulations, we derive alternate hinge elements capable of translocation in vitro and in vivo and describe their effects on the conformational trajectory of the EF-G-bound, translocating ribosome. In these alternate conformational pathways, we observe a diversity of swivel kinetics, hinge motions, three-dimensional head domain trajectories and tRNA dynamics. By finding alternate conformational pathways of translocation, we identify motions and intermediates that are essential or malleable in this process. These findings highlight the plasticity of protein synthesis and provide a more thorough understanding of the available sequence and conformational landscape of a central biological process.
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Affiliation(s)
- Jose L. Alejo
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dylan Girodat
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Michael J. Hammerling
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Jessica A. Willi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, United States of America
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Aaron E. Engelhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Katarzyna P. Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
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2
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Bao L, Liljeruhm J, Crespo Blanco R, Brandis G, Remme J, Forster AC. Translational impacts of enzymes that modify ribosomal RNA around the peptidyl transferase centre. RNA Biol 2024; 21:31-41. [PMID: 38952121 PMCID: PMC11221467 DOI: 10.1080/15476286.2024.2368305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/11/2024] [Indexed: 07/03/2024] Open
Abstract
Large ribosomal RNAs (rRNAs) are modified heavily post-transcriptionally in functionally important regions but, paradoxically, individual knockouts (KOs) of the modification enzymes have minimal impact on Escherichia coli growth. Furthermore, we recently constructed a strain with combined KOs of five modification enzymes (RluC, RlmKL, RlmN, RlmM and RluE) of the 'critical region' of the peptidyl transferase centre (PTC) in 23S rRNA that exhibited only a minor growth defect at 37°C (although major at 20°C). However, our combined KO of modification enzymes RluC and RlmE (not RluE) resulted in conditional lethality (at 20°C). Although the growth rates for both multiple-KO strains were characterized, the molecular explanations for such deficits remain unclear. Here, we pinpoint biochemical defects in these strains. In vitro fast kinetics at 20°C and 37°C with ribosomes purified from both strains revealed, counterintuitively, the slowing of translocation, not peptide bond formation or peptidyl release. Elongation rates of protein synthesis in vivo, as judged by the kinetics of β-galactosidase induction, were also slowed. For the five-KO strain, the biggest deficit at 37°C was in 70S ribosome assembly, as judged by a dominant 50S peak in ribosome sucrose gradient profiles at 5 mM Mg2+. Reconstitution of this 50S subunit from purified five-KO rRNA and ribosomal proteins supported a direct role in ribosome biogenesis of the PTC region modifications per se, rather than of the modification enzymes. These results clarify the importance and roles of the enigmatic rRNA modifications.
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Affiliation(s)
- Letian Bao
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Josefine Liljeruhm
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Rubén Crespo Blanco
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Gerrit Brandis
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jaanus Remme
- Department of Molecular Biology, University of Tartu, Tartu, Estonia
| | - Anthony C. Forster
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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3
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Zilberzwige-Tal S, Fontanarrosa P, Bychenko D, Dorfan Y, Gazit E, Myers CJ. Investigating and Modeling the Factors That Affect Genetic Circuit Performance. ACS Synth Biol 2023; 12:3189-3204. [PMID: 37916512 PMCID: PMC10661042 DOI: 10.1021/acssynbio.3c00151] [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: 03/11/2023] [Indexed: 11/03/2023]
Abstract
Over the past 2 decades, synthetic biology has yielded ever more complex genetic circuits that are able to perform sophisticated functions in response to specific signals. Yet, genetic circuits are not immediately transferable to an outside-the-lab setting where their performance is highly compromised. We propose introducing a broader test step to the design-build-test-learn workflow to include factors that might contribute to unexpected genetic circuit performance. As a proof of concept, we have designed and evaluated a genetic circuit in various temperatures, inducer concentrations, nonsterilized soil exposure, and bacterial growth stages. We determined that the circuit's performance is dramatically altered when these factors differ from the optimal lab conditions. We observed significant changes in the time for signal detection as well as signal intensity when the genetic circuit was tested under nonoptimal lab conditions. As a learning effort, we then proceeded to generate model predictions in untested conditions, which is currently lacking in synthetic biology application design. Furthermore, broader test and learn steps uncovered a negative correlation between the time it takes for a gate to turn ON and the bacterial growth phases. As the synthetic biology discipline transitions from proof-of-concept genetic programs to appropriate and safe application implementations, more emphasis on test and learn steps (i.e., characterizing parts and circuits for a broad range of conditions) will provide missing insights on genetic circuit behavior outside the lab.
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Affiliation(s)
- Shai Zilberzwige-Tal
- The
Shmunis School of Biomedicine and Cancer Research, Life Sciences Faculty, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel
| | - Pedro Fontanarrosa
- Department
of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Darya Bychenko
- The
Shmunis School of Biomedicine and Cancer Research, Life Sciences Faculty, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel
| | - Yuval Dorfan
- Department
of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Bio-engineering,
Electrical Engineering Faculty, Holon Institute
of Technology (HIT), Holon 5810201, Israel
- Alagene
Ltd., Innovation Center, Reichman University, Herzliya 7670608, Israel
| | - Ehud Gazit
- The
Shmunis School of Biomedicine and Cancer Research, Life Sciences Faculty, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel
| | - Chris J. Myers
- Department
of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
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4
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Chung KP, Loiacono FV, Neupert J, Wu M, Bock R. An RNA thermometer in the chloroplast genome of Chlamydomonas facilitates temperature-controlled gene expression. Nucleic Acids Res 2023; 51:11386-11400. [PMID: 37855670 PMCID: PMC10639063 DOI: 10.1093/nar/gkad816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/01/2023] [Accepted: 09/20/2023] [Indexed: 10/20/2023] Open
Abstract
Riboregulators such as riboswitches and RNA thermometers provide simple, protein-independent tools to control gene expression at the post-transcriptional level. In bacteria, RNA thermometers regulate protein synthesis in response to temperature shifts. Thermometers outside of the bacterial world are rare, and in organellar genomes, no RNA thermometers have been identified to date. Here we report the discovery of an RNA thermometer in a chloroplast gene of the unicellular green alga Chlamydomonas reinhardtii. The thermometer, residing in the 5' untranslated region of the psaA messenger RNA forms a hairpin-type secondary structure that masks the Shine-Dalgarno sequence at 25°C. At 40°C, melting of the secondary structure increases accessibility of the Shine-Dalgarno sequence to initiating ribosomes, thus enhancing protein synthesis. By targeted nucleotide substitutions and transfer of the thermometer into Escherichia coli, we show that the secondary structure is necessary and sufficient to confer the thermometer properties. We also demonstrate that the thermometer provides a valuable tool for inducible transgene expression from the Chlamydomonas plastid genome, in that a simple temperature shift of the algal culture can greatly increase recombinant protein yields.
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Affiliation(s)
- Kin Pan Chung
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - F Vanessa Loiacono
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Juliane Neupert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mengting Wu
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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5
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Saroha P, Rathore AS. Production of bioactive recombinant monoclonal antibody fragment in periplasm of Escherichia coli expression system. Prep Biochem Biotechnol 2023; 53:1288-1296. [PMID: 37040146 DOI: 10.1080/10826068.2023.2195482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
The microbial expression system (Escherichia coli) is the most widely studied host for the production of biotherapeutic products, such as antibody fragments, single chain variable fragments and nanobodies. However, recombinant biotherapeutic proteins are often expressed as insoluble proteins, thereby limiting the utility of E. coli as expression system. To overcome this limitation, various strategies have been developed, such as changes at DNA level (codon optimization), fusion with soluble tags and variations in process parameters (temperature), and inducer concentration. However, there is no "one size fits all" strategy. The most commonly used approach involves induction at low temperature, as reducing the temperature during cultivation has been reported to increase bioactive protein production in E. coli. In this study, we examine the impact of various process parameters, such as temperature and inducer concentration, as well as, high plasmid copy number vector for achieving enhanced soluble expression of TNFα inhibitor Fab. An interaction amongst these parameters has been observed and their optimization has been demonstrated to result in expression of 30 ± 3 mg/L antibody fragment using E. coli. This case study illustrates how process optimization can contribute toward making biotherapeutics affordable.
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Affiliation(s)
- Preeti Saroha
- Department of Chemical Engineering, Indian Institute of Technology, Delhi, New Delhi, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology, Delhi, New Delhi, India
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6
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Flores ME, Jafarzadeh A, Moghadam SV, Vadde KK, Dhar DA, Nunu RR, Kapoor V. Occurrence and removal of fecal bacteria and microbial source tracking markers in a stormwater detention basin overlying the Edwards Aquifer recharge zone in Texas. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:103836-103850. [PMID: 37691063 DOI: 10.1007/s11356-023-29636-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
The Edwards Aquifer is the primary water resource for over 2 million people in Texas and faces challenges including fecal contamination of water recharging the aquifer, while effectiveness of best management practices (BMPs) such as detention basins in mitigating fecal pollution remains poorly understood. For this study, the inlet and outlet of a detention basin overlying the aquifer's recharge zone were sampled following storm events using automated samplers. Microbial source tracking and culture-based methods were used to determine the occurrence and removal of fecal genetic markers and fecal coliform bacteria in collected water samples. Markers included E. coli (EC23S857), Enterococcus (Entero1), human (HF183), canine (BacCan), and bird (GFD). Fecal coliforms, EC23S857, and Entero1 were detected following each storm event. GFD was the most frequent host-associated marker detected (91% of samples), followed by BacCan (46%), and HF183 (17%). Wilcoxon signed rank tests indicated significantly lower outlet concentrations for fecal coliforms, EC23S857, and Entero1, but not for HF183, GFD, and BacCan. Higher GFD and BacCan outlet concentrations may be due to factors independent of basin design, such as the non-point source nature of bird fecal contamination and domestic dog care practices in neighborhoods contributing to the basin. Mann-Whitney tests showed marker concentrations were not significantly higher during instances of fecal coliform water quality criterion exceedance, except for E. coli, and that fecal coliform concentrations were not significantly different based on marker detection. Overall, results suggest that the detention basin is effective in attenuating fecal contamination associated with fecal coliforms and the general markers, but not for host-associated markers. Consequently, management efforts should focus on mitigating dog and bird-associated fecal pollution in the study region.
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Affiliation(s)
- Mauricio Eduardo Flores
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
- Southwest Research Institute, 6220 Culebra Rd, San Antonio, TX, 78238, USA
| | - Arash Jafarzadeh
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Sina Vedadi Moghadam
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Kiran Kumar Vadde
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Dipti Anik Dhar
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Rebecca R Nunu
- Southwest Research Institute, 6220 Culebra Rd, San Antonio, TX, 78238, USA
| | - Vikram Kapoor
- School of Civil & Environmental Engineering, and Construction Management, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA.
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7
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Matamouros S, Gensch T, Cerff M, Sachs CC, Abdollahzadeh I, Hendriks J, Horst L, Tenhaef N, Tenhaef J, Noack S, Graf M, Takors R, Nöh K, Bott M. Growth-rate dependency of ribosome abundance and translation elongation rate in Corynebacterium glutamicum differs from that in Escherichia coli. Nat Commun 2023; 14:5611. [PMID: 37699882 PMCID: PMC10497606 DOI: 10.1038/s41467-023-41176-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
Bacterial growth rate (µ) depends on the protein synthesis capacity of the cell and thus on the number of active ribosomes and their translation elongation rate. The relationship between these fundamental growth parameters have only been described for few bacterial species, in particular Escherichia coli. Here, we analyse the growth-rate dependency of ribosome abundance and translation elongation rate for Corynebacterium glutamicum, a gram-positive model species differing from E. coli by a lower growth temperature optimum and a lower maximal growth rate. We show that, unlike in E. coli, there is little change in ribosome abundance for µ <0.4 h-1 in C. glutamicum and the fraction of active ribosomes is kept above 70% while the translation elongation rate declines 5-fold. Mathematical modelling indicates that the decrease in the translation elongation rate can be explained by a depletion of translation precursors.
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Affiliation(s)
- Susana Matamouros
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
| | - Thomas Gensch
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin Cerff
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Christian C Sachs
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Iman Abdollahzadeh
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Johnny Hendriks
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Lucas Horst
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Julia Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michaela Graf
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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8
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Knapp BD, Willis L, Gonzalez C, Vashistha H, Touma JJ, Tikhonov M, Ram J, Salman H, Elias JE, Huang KC. Metabolomic rearrangement controls the intrinsic microbial response to temperature changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.22.550177. [PMID: 37546722 PMCID: PMC10401945 DOI: 10.1101/2023.07.22.550177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Temperature is one of the key determinants of microbial behavior and survival, whose impact is typically studied under heat- or cold-shock conditions that elicit specific regulation to combat lethal stress. At intermediate temperatures, cellular growth rate varies according to the Arrhenius law of thermodynamics without stress responses, a behavior whose origins have not yet been elucidated. Using single-cell microscopy during temperature perturbations, we show that bacteria exhibit a highly conserved, gradual response to temperature upshifts with a time scale of ~1.5 doublings at the higher temperature, regardless of initial/final temperature or nutrient source. We find that this behavior is coupled to a temperature memory, which we rule out as being neither transcriptional, translational, nor membrane dependent. Instead, we demonstrate that an autocatalytic enzyme network incorporating temperature-sensitive Michaelis-Menten kinetics recapitulates all temperature-shift dynamics through metabolome rearrangement, which encodes a temperature memory and successfully predicts alterations in the upshift response observed under simple-sugar, low-nutrient conditions, and in fungi. This model also provides a mechanistic framework for both Arrhenius-dependent growth and the classical Monod Equation through temperature-dependent metabolite flux.
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Affiliation(s)
| | - Lisa Willis
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Carlos Gonzalez
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Harsh Vashistha
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Joanna Jammal Touma
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mikhail Tikhonov
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jeffrey Ram
- Department of Physiology, Wayne State University, Detroit, MI 48201, USA
| | - Hanna Salman
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Josh E. Elias
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Kerwyn Casey Huang
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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9
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Llop A, Bibak S, Cantos R, Salinas P, Contreras A. The ribosome assembly GTPase EngA is involved in redox signaling in cyanobacteria. Front Microbiol 2023; 14:1242616. [PMID: 37637111 PMCID: PMC10448771 DOI: 10.3389/fmicb.2023.1242616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Photosynthetic organisms must cope with environmental challenges, like those imposed by the succession of days and nights or by sudden changes in light intensities, that trigger global changes in gene expression and metabolism. The photosynthesis machinery is particularly susceptible to environmental changes and adaptation to them often involves redox-sensing proteins that are the targets of reactive oxygen species generated by photosynthesis activity. Here we show that EngA, an essential GTPase and ribosome-assembly protein involved in ribosome biogenesis in bacteria and chloroplasts, also plays a role in acclimatization to environmentally relevant stress in Synechococcus elongatus PCC7942 and that PipX, a promiscuous regulatory protein that binds to EngA, appears to fine-tune EngA activity. During growth in cold or high light conditions, the EngA levels rise, with a concomitant increase of the EngA/PipX ratio. However, a sudden increase in light intensity turns EngA into a growth inhibitor, a response involving residue Cys122 of EngA, which is part of the GD1-G4 motif NKCES of EngA proteins, with the cysteine conserved just in the cyanobacteria-chloroplast lineage. This work expands the repertoire of ribosome-related factors transmitting redox signals in photosynthetic organisms and provides additional insights into the complexity of the regulatory interactions mediated by EngA and PipX.
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Affiliation(s)
| | | | | | | | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
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10
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Joiret M, Kerff F, Rapino F, Close P, Geris L. A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome and its significance for the elongation cycle kinetics. Comput Struct Biotechnol J 2023; 21:3768-3795. [PMID: 37560126 PMCID: PMC10407619 DOI: 10.1016/j.csbj.2023.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023] Open
Abstract
The central function of the large subunit of the ribosome is to catalyze peptide bond formation. This biochemical reaction is conducted at the peptidyl transferase center (PTC). Experimental evidence shows that the catalytic activity is affected by the electrostatic environment around the peptidyl transferase center. Here, we set up a minimal geometrical model fitting the available x-ray solved structures of the ribonucleic cavity around the catalytic center of the large subunit of the ribosome. The purpose of this phenomenological model is to estimate quantitatively the electrostatic potential and electric field that are experienced during the peptidyl transfer reaction. At least two reasons motivate the need for developing this quantification. First, we inquire whether the electric field in this particular catalytic environment, made only of nucleic acids, is of the same order of magnitude as the one prevailing in catalytic centers of the proteic enzymes counterparts. Second, the protein synthesis rate is dependent on the nature of the amino acid sequentially incorporated in the nascent chain. The activation energy of the catalytic reaction and its detailed kinetics are shown to be dependent on the mechanical work exerted on the amino acids by the electric field, especially when one of the four charged amino acid residues (R, K, E, D) has previously been incorporated at the carboxy-terminal end of the peptidyl-tRNA. Physical values of the electric field provide quantitative knowledge of mechanical work, activation energy and rate of the peptide bond formation catalyzed by the ribosome. We show that our theoretical calculations are consistent with two independent sets of previously published experimental results. Experimental results for E.coli in the minimal case of the dipeptide bond formation when puromycin is used as the final amino acid acceptor strongly support our theoretically derived reaction time courses. Experimental Ribo-Seq results on E. coli and S. cerevisiae comparing the residence time distribution of ribosomes upon specific codons are also well accounted for by our theoretical calculations. The statistical queueing time theory was used to model the ribosome residence time per codon during nascent protein elongation and applied for the interpretation of the Ribo-Seq data. The hypo-exponential distribution fits the residence time observed distribution of the ribosome on a codon. An educated deconvolution of this distribution is used to estimate the rates of each elongation step in a codon specific manner. Our interpretation of all these results sheds light on the functional role of the electrostatic profile around the PTC and its impact on the ribosome elongation cycle.
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Affiliation(s)
- Marc Joiret
- Biomechanics Research Unit, GIGA in silico medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
| | - Frederic Kerff
- UR InBios Centre d'Ingénierie des Protéines, Liège University, Bât B6a, Allèe du 6 Août, 19, B-4000 Liège, Belgium
| | - Francesca Rapino
- Cancer Signaling, GIGA Stem Cells, Liège University, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Pierre Close
- Cancer Signaling, GIGA Stem Cells, Liège University, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Liesbet Geris
- Biomechanics Research Unit, GIGA in silico medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
- Skeletal Biology & Engineering Research Center, KU Leuven, ON I Herestraat 49 - box 813, 3000 Leuven, Belgium
- Biomechanics Section, KU Leuven, Celestijnenlaan 300C box 2419, B-3001 Heverlee, Belgium
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11
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Wang X, Wang J, Zhang X, Zhang J, Zhou Y, Wang F, Li X. Efficient Myrcene Production Using Linalool Dehydratase Isomerase and Rational Biochemical Process in Escherichia coli. J Biotechnol 2023:S0168-1656(23)00113-X. [PMID: 37285942 DOI: 10.1016/j.jbiotec.2023.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023]
Abstract
Microbial synthesis of plant-based myrcene is of great interest because of its high demand, however, achieving high biosynthetic titers remains a great challenge. Previous strategies adopted for microbial myrcene production have relied on the recruitment of a multi-step biosynthetic pathway which requires complex metabolic regulation or high activity of myrcene synthase, hindering its application. Here, we present an effective one-step biotransformation system for myrcene biosynthesis from geraniol, using a linalool dehydratase isomerase (LDI) to overcome these limitations. The truncated LDI possesses nominal activity that catalyzes the isomerization of geraniol to linalool and the subsequent dehydration to myrcene in anaerobic environment. In order to improve the robustness of engineered strains for the efficient conversion of geraniol to myrcene, rational enzyme modification and a series of biochemical process engineering were employed to maintain and improve the anaerobic catalytic activity of LDI. Finally, by introducing the optimized myrcene biosynthetic capability in the existing geraniol-production strain, we achieve de novo biosynthesis of myrcene at 1.25g/L from glycerol during 84h aerobic-anaerobic two-stage fermentation, which is much higher than previously reported myrcene levels. This work highlights the value of dehydratase isomerase-based biocatalytic in establishing novel biosynthetic pathways and lays a reliable foundation for the microbial synthesis of myrcene.
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Affiliation(s)
- Xun Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Jiajie Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Xinyi Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Jia Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Yujunjie Zhou
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Fei Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Xun Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China.
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12
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Moon S, Ham S, Jeong J, Ku H, Kim H, Lee C. Temperature Matters: Bacterial Response to Temperature Change. J Microbiol 2023; 61:343-357. [PMID: 37010795 DOI: 10.1007/s12275-023-00031-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 04/04/2023]
Abstract
Temperature is one of the most important factors in all living organisms for survival. Being a unicellular organism, bacterium requires sensitive sensing and defense mechanisms to tolerate changes in temperature. During a temperature shift, the structure and composition of various cellular molecules including nucleic acids, proteins, and membranes are affected. In addition, numerous genes are induced during heat or cold shocks to overcome the cellular stresses, which are known as heat- and cold-shock proteins. In this review, we describe the cellular phenomena that occur with temperature change and bacterial responses from a molecular perspective, mainly in Escherichia coli.
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Affiliation(s)
- Seongjoon Moon
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Soojeong Ham
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Juwon Jeong
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Heechan Ku
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Hyunhee Kim
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea.
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea.
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13
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Bravo P, Lung Ng S, MacGillivray KA, Hammer BK, Yunker PJ. Vertical growth dynamics of biofilms. Proc Natl Acad Sci U S A 2023; 120:e2214211120. [PMID: 36881625 PMCID: PMC10089195 DOI: 10.1073/pnas.2214211120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/02/2023] [Indexed: 03/08/2023] Open
Abstract
During the biofilm life cycle, bacteria attach to a surface and then reproduce, forming crowded, growing communities. Many theoretical models of biofilm growth dynamics have been proposed; however, difficulties in accurately measuring biofilm height across relevant time and length scales have prevented testing these models, or their biophysical underpinnings, empirically. Using white light interferometry, we measure the heights of microbial colonies with nanometer precision from inoculation to their final equilibrium height, producing a detailed empirical characterization of vertical growth dynamics. We propose a heuristic model for vertical growth dynamics based on basic biophysical processes inside a biofilm: diffusion and consumption of nutrients and growth and decay of the colony. This model captures the vertical growth dynamics from short to long time scales (10 min to 14 d) of diverse microorganisms, including bacteria and fungi.
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Affiliation(s)
- Pablo Bravo
- School of Physics, Georgia Institute of Technology, Atlanta, GA30332
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA30332
| | - Siu Lung Ng
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332
| | - Kathryn A. MacGillivray
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA30332
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332
| | - Brian K. Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332
| | - Peter J. Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, GA30332
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14
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Ngugi DK, Acinas SG, Sánchez P, Gasol JM, Agusti S, Karl DM, Duarte CM. Abiotic selection of microbial genome size in the global ocean. Nat Commun 2023; 14:1384. [PMID: 36914646 PMCID: PMC10011403 DOI: 10.1038/s41467-023-36988-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.
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Affiliation(s)
- David K Ngugi
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona, Spain
| | - Susana Agusti
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
| | - David M Karl
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaií at Mãnoa, Honolulu, USA
| | - Carlos M Duarte
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal, Saudi Arabia
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15
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Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
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Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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16
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Giuliodori AM, Belardinelli R, Duval M, Garofalo R, Schenckbecher E, Hauryliuk V, Ennifar E, Marzi S. Escherichia coli CspA stimulates translation in the cold of its own mRNA by promoting ribosome progression. Front Microbiol 2023; 14:1118329. [PMID: 36846801 PMCID: PMC9947658 DOI: 10.3389/fmicb.2023.1118329] [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: 12/07/2022] [Accepted: 01/06/2023] [Indexed: 02/11/2023] Open
Abstract
Escherichia coli CspA is an RNA binding protein that accumulates during cold-shock and stimulates translation of several mRNAs-including its own. Translation in the cold of cspA mRNA involves a cis-acting thermosensor element, which enhances ribosome binding, and the trans-acting action of CspA. Using reconstituted translation systems and probing experiments we show that, at low temperature, CspA specifically promotes the translation of the cspA mRNA folded in the conformation less accessible to the ribosome, which is formed at 37°C but is retained upon cold shock. CspA interacts with its mRNA without inducing large structural rearrangements, but allowing the progression of the ribosomes during the transition from translation initiation to translation elongation. A similar structure-dependent mechanism may be responsible for the CspA-dependent translation stimulation observed with other probed mRNAs, for which the transition to the elongation phase is progressively facilitated during cold acclimation with the accumulation of CspA.
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Affiliation(s)
- Anna Maria Giuliodori
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy,*Correspondence: Anna Maria Giuliodori, ✉
| | - Riccardo Belardinelli
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Melodie Duval
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Raffaella Garofalo
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Emma Schenckbecher
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden,Institute of Technology, University of Tartu, Tartu, Estonia
| | - Eric Ennifar
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l’ARN, CNRS 9002, Université de Strasbourg, Strasbourg, France,Stefano Marzi, ✉
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17
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Shao G, He T, Mu Y, Mu P, Ao J, Lin X, Ruan L, Wang Y, Gao Y, Liu D, Zhang L, Chen X. The genome of a hadal sea cucumber reveals novel adaptive strategies to deep-sea environments. iScience 2022; 25:105545. [PMID: 36444293 PMCID: PMC9700323 DOI: 10.1016/j.isci.2022.105545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/18/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
How organisms cope with coldness and high pressure in the hadal zone remains poorly understood. Here, we sequenced and assembled the genome of hadal sea cucumber Paelopatides sp. Yap with high quality and explored its potential mechanisms for deep-sea adaptation. First, the expansion of ACOX1 for rate-limiting enzyme in the DHA synthesis pathway, increased DHA content in the phospholipid bilayer, and positive selection of EPT1 may maintain cell membrane fluidity. Second, three genes for translation initiation factors and two for ribosomal proteins underwent expansion, and three ribosomal protein genes were positively selected, which may ameliorate the protein synthesis inhibition or ribosome dissociation in the hadal zone. Third, expansion and positive selection of genes associated with stalled replication fork recovery and DNA repair suggest improvements in DNA protection. This is the first genome sequence of a hadal invertebrate. Our results provide insights into the genetic adaptations used by invertebrate in deep oceans.
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Affiliation(s)
- Guangming Shao
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Tianliang He
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yinnan Mu
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Pengfei Mu
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jingqun Ao
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xihuang Lin
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
| | - Lingwei Ruan
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
| | - YuGuang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
| | - Yuan Gao
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Dinggao Liu
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong 519000, China
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18
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Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations. mSystems 2022; 7:e0058822. [PMID: 35950761 PMCID: PMC9426432 DOI: 10.1128/msystems.00588-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in nonmesophilic organisms, however, is currently missing. In this study, thermodynamically constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella psychrophila WP2, under suboptimal (4°C), optimal (15°C), and supraoptimal (20°C) growth temperatures. The models were calibrated with experimentally determined growth rates of WP2. Gibbs free energy change of reactions (ΔrG'), metabolic fluxes, and metabolite concentrations were predicted using random simulations to characterize temperature-dependent changes in the metabolism. The modeling revealed the highest metabolic efficiency at the optimal temperature, and it suggested distinct patterns of ATP production and consumption that could lead to lower metabolic efficiency under suboptimal or supraoptimal temperatures. The modeling also predicted rearrangement of fluxes through multiple metabolic pathways, including the glycolysis pathway, Entner-Doudoroff pathway, tricarboxylic acid (TCA) cycle, and electron transport system, and these predictions were corroborated through comparisons to WP2 transcriptomes. Furthermore, predictions of metabolite concentrations revealed the potential conservation of reducing equivalents and ATP in the suboptimal temperature, consistent with experimental observations from other psychrophiles. Taken together, the WP2 models provided mechanistic insights into the metabolism of a psychrophile in response to different temperatures. IMPORTANCE Metabolic flexibility is a central component of any organism's ability to survive and adapt to changes in environmental conditions. This study represents the first application of thermodynamically constrained genome-scale models in simulating the metabolic responses of a deep-sea psychrophilic bacterium to various temperatures. The models predicted differences in metabolic efficiency that were attributed to changes in metabolic pathway utilization and metabolite concentration during growth under optimal and nonoptimal temperatures. Experimental growth measurements were used for model calibration, and temperature-dependent transcriptomic changes corroborated the model-predicted rearrangement of metabolic fluxes. Overall, this study highlights the utility of modeling approaches in studying the temperature-driven metabolic responses of an extremophilic organism.
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19
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Dash S, Palma CSD, Baptista ISC, Almeida BLB, Bahrudeen MNM, Chauhan V, Jagadeesan R, Ribeiro AS. Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli. Nucleic Acids Res 2022; 50:8512-8528. [PMID: 35920318 PMCID: PMC9410904 DOI: 10.1093/nar/gkac643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
Cold shock adaptability is a key survival skill of gut bacteria of warm-blooded animals. Escherichia coli cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms. Having identified short-term, cold shock repressed genes, we show that their responsiveness is unrelated to their transcription factors or global regulators, while their single-cell protein numbers' variability increases after cold shock. We hypothesized that some cold shock repressed genes could be triggered by high propensity for transcription locking due to changes in DNA supercoiling (likely due to DNA relaxation caused by an overall reduction in negative supercoiling). Concomitantly, we found that nearly half of cold shock repressed genes are also highly responsive to gyrase inhibition (albeit most genes responsive to gyrase inhibition are not cold shock responsive). Further, their response strengths to cold shock and gyrase inhibition correlate. Meanwhile, under cold shock, nucleoid density increases, and gyrases and nucleoid become more colocalized. Moreover, the cellular energy decreases, which may hinder positive supercoils resolution. Overall, we conclude that sensitivity to diminished negative supercoiling is a core feature of E. coli's short-term, cold shock transcriptional program, and could be used to regulate the temperature sensitivity of synthetic circuits.
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Affiliation(s)
- Suchintak Dash
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Cristina S D Palma
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Ines S C Baptista
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Bilena L B Almeida
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Mohamed N M Bahrudeen
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Vatsala Chauhan
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Rahul Jagadeesan
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Andre S Ribeiro
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland.,Center of Technology and Systems (CTS-Uninova), NOVA University of Lisbon 2829-516, Monte de Caparica, Portugal
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20
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Wu D, Wang H, Ouyang Q. Robust network topologies for temperature-inducible bioswitches. J Biol Eng 2022; 16:12. [PMID: 35606858 PMCID: PMC9128120 DOI: 10.1186/s13036-022-00290-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Thermoinducible bioswitches are unique in that the all-or-none switch response is triggered by temperature, which is a global factor that impacts all biochemical reaction processes. To date, temperature-inducible bioswitches rely exclusively on special thermal sensing biomolecules of DNA, RNA, proteins and lipids whose conformations are critically temperature dependent. METHOD This paper extends the traditional thermal switch by utilizing purposely designed network topologies of biomolecular interactions to achieve the switching function. By assuming the general Arrhenius law for biochemical reactions, we explore the full space of all three-node genetic interaction networks to screen topologies capable of thermal bioswitches. Three target bioswitches, i.e., thermal-inducible Off-On, cold-inducible On-Off, and hybrid Off-On-Off double switches, are considered separately. CONCLUSIONS We identify the minimal and core network skeletons that are basic and essential for building robust high-performance bioswitches: three Off-On motifs, three On-Off motifs, and an incoherent feedforward motif for an Off-On-Off double switch. Functional topologies are implicitly preferential in choosing parameter values to achieve the target functions. The scenario of the topology-based bioswitch we propose here is an extension of molecule-based bioswitches and would be valuable in aiding the rational design and synthesis of efficient high-performance thermal bioswitches.
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Affiliation(s)
- Di Wu
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Hongli Wang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China. .,Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| | - Qi Ouyang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, Peking University, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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21
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Investigation of the Relation between Temperature and M13 Phage Production via ATP Expenditure. Processes (Basel) 2022. [DOI: 10.3390/pr10050962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
M13 bacteriophage is a promising biomolecule capable of various bionano and material science applications. The biomaterial can self-assemble into matrices to fabricate bioscaffolds using high phage concentration and high phage purity. Previous studies aimed to acquire these conditions in large-scale phage production and have identified the optimal culture temperature range at 28–31 °C. However, explanations as to why this temperature range was optimal for phage production is absent from the work. Therefore, in this study, we identified the relation between culture temperature and M13 phage production using ATP expenditure calculations to comprehend the high yield phage production at the optimal temperature range. We extended a coarse-grained model for the evaluation of phage protein and ribosomal protein synthesis with the premise that phage proteins (a ribosomal protein) are translated by bacterial ribosomes in E. coli through expenditure of ATP energy. By comparing the ATP energy for ribosomal protein synthesis estimated using the coarse-grained model and the experimentally calculated ATP expenditure for phage production, we interpreted the high phage yield at the optimal temperature range and recognized ATP analysis as a reasonable method that can be used to evaluate other parameters for phage production optimization.
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22
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Abstract
Temperature impacts biological systems across all length and timescales. Cells and the enzymes that comprise them respond to temperature fluctuations on short timescales, and temperature can affect protein folding, the molecular composition of cells, and volume expansion. Entire ecosystems exhibit temperature-dependent behaviors, and global warming threatens to disrupt thermal homeostasis in microbes that are important for human and planetary health. Intriguingly, the growth rate of most species follows the Arrhenius law of equilibrium thermodynamics, with an activation energy similar to that of individual enzymes but with maximal growth rates and over temperature ranges that are species specific. In this review, we discuss how the temperature dependence of critical cellular processes, such as the central dogma and membrane fluidity, contributes to the temperature dependence of growth. We conclude with a discussion of adaptation to temperature shifts and the effects of temperature on evolution and on the properties of microbial ecosystems.
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Affiliation(s)
- Benjamin D Knapp
- Biophysics Program, Stanford University School of Medicine, Stanford, California, USA;
| | - Kerwyn Casey Huang
- Biophysics Program, Stanford University School of Medicine, Stanford, California, USA; .,Department of Bioengineering, Stanford University, Stanford, California, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
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23
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Gao Y, Thiele W, Saleh O, Scossa F, Arabi F, Zhang H, Sampathkumar A, Kühn K, Fernie A, Bock R, Schöttler MA, Zoschke R. Chloroplast translational regulation uncovers nonessential photosynthesis genes as key players in plant cold acclimation. THE PLANT CELL 2022; 34:2056-2079. [PMID: 35171295 PMCID: PMC9048916 DOI: 10.1093/plcell/koac056] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/12/2022] [Indexed: 05/04/2023]
Abstract
Plants evolved efficient multifaceted acclimation strategies to cope with low temperatures. Chloroplasts respond to temperature stimuli and participate in temperature sensing and acclimation. However, very little is known about the involvement of chloroplast genes and their expression in plant chilling tolerance. Here we systematically investigated cold acclimation in tobacco seedlings over 2 days of exposure to low temperatures by examining responses in chloroplast genome copy number, transcript accumulation and translation, photosynthesis, cell physiology, and metabolism. Our time-resolved genome-wide investigation of chloroplast gene expression revealed substantial cold-induced translational regulation at both the initiation and elongation levels, in the virtual absence of changes at the transcript level. These cold-triggered dynamics in chloroplast translation are widely distinct from previously described high light-induced effects. Analysis of the gene set responding significantly to the cold stimulus suggested nonessential plastid-encoded subunits of photosynthetic protein complexes as novel players in plant cold acclimation. Functional characterization of one of these cold-responsive chloroplast genes by reverse genetics demonstrated that the encoded protein, the small cytochrome b6f complex subunit PetL, crucially contributes to photosynthetic cold acclimation. Together, our results uncover an important, previously underappreciated role of chloroplast translational regulation in plant cold acclimation.
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Affiliation(s)
- Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Wolfram Thiele
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Omar Saleh
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Council for Agricultural Research and Economics, Research Center for Genomics and Bioinformatics (CREA-GB), Rome, 00178, Italy
| | - Fayezeh Arabi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Hongmou Zhang
- Institute of Optical Sensor Systems, German Aerospace Center (DLR), Berlin, 12489, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Kristina Kühn
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Mark A Schöttler
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
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Gao Y, Thiele W, Saleh O, Scossa F, Arabi F, Zhang H, Sampathkumar A, Kühn K, Fernie A, Bock R, Schöttler MA, Zoschke R. Chloroplast translational regulation uncovers nonessential photosynthesis genes as key players in plant cold acclimation. THE PLANT CELL 2022; 34:2056-2079. [PMID: 35171295 DOI: 10.1093/plcell/koac056%jtheplantcell] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/12/2022] [Indexed: 05/28/2023]
Abstract
Plants evolved efficient multifaceted acclimation strategies to cope with low temperatures. Chloroplasts respond to temperature stimuli and participate in temperature sensing and acclimation. However, very little is known about the involvement of chloroplast genes and their expression in plant chilling tolerance. Here we systematically investigated cold acclimation in tobacco seedlings over 2 days of exposure to low temperatures by examining responses in chloroplast genome copy number, transcript accumulation and translation, photosynthesis, cell physiology, and metabolism. Our time-resolved genome-wide investigation of chloroplast gene expression revealed substantial cold-induced translational regulation at both the initiation and elongation levels, in the virtual absence of changes at the transcript level. These cold-triggered dynamics in chloroplast translation are widely distinct from previously described high light-induced effects. Analysis of the gene set responding significantly to the cold stimulus suggested nonessential plastid-encoded subunits of photosynthetic protein complexes as novel players in plant cold acclimation. Functional characterization of one of these cold-responsive chloroplast genes by reverse genetics demonstrated that the encoded protein, the small cytochrome b6f complex subunit PetL, crucially contributes to photosynthetic cold acclimation. Together, our results uncover an important, previously underappreciated role of chloroplast translational regulation in plant cold acclimation.
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Affiliation(s)
- Yang Gao
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Wolfram Thiele
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Omar Saleh
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Council for Agricultural Research and Economics, Research Center for Genomics and Bioinformatics (CREA-GB), Rome, 00178, Italy
| | - Fayezeh Arabi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Hongmou Zhang
- Institute of Optical Sensor Systems, German Aerospace Center (DLR), Berlin, 12489, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Kristina Kühn
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Mark A Schöttler
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
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25
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Metelev M, Lundin E, Volkov IL, Gynnå AH, Elf J, Johansson M. Direct measurements of mRNA translation kinetics in living cells. Nat Commun 2022; 13:1852. [PMID: 35388013 PMCID: PMC8986856 DOI: 10.1038/s41467-022-29515-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 03/17/2022] [Indexed: 01/09/2023] Open
Abstract
Ribosome mediated mRNA translation is central to life. The cycle of translation, however, has been characterized mostly using reconstituted systems, with only few techniques applicable for studies in the living cell. Here we describe a live-cell ribosome-labeling method, which allows us to characterize the whole processes of finding and translating an mRNA, using single-molecule tracking techniques. We find that more than 90% of both bacterial ribosomal subunits are engaged in translation at any particular time, and that the 30S and 50S ribosomal subunits spend the same average time bound to an mRNA, revealing that 30S re-initiation on poly-cistronic mRNAs is not prevalent in E. coli. Instead, our results are best explained by substantial 70S re-initiation of translation of poly-cistronic mRNAs, which is further corroborated by experiments with translation initiation inhibitors. Finally, we find that a variety of previously described orthogonal ribosomes, with altered anti-Shine-Dalgarno sequences, show significant binding to endogenous mRNAs.
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Affiliation(s)
- Mikhail Metelev
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Erik Lundin
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Ivan L Volkov
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Arvid H Gynnå
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Magnus Johansson
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
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26
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Lipničanová S, Legerská B, Chmelová D, Ondrejovič M, Miertuš S. Optimization of an Inclusion Body-Based Production of the Influenza Virus Neuraminidase in Escherichia coli. Biomolecules 2022; 12:331. [PMID: 35204831 PMCID: PMC8869668 DOI: 10.3390/biom12020331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
Neuraminidase (NA), as an important protein of influenza virus, represents a promising target for the development of new antiviral agents for the treatment and prevention of influenza A and B. Bacterial host strain Escherichia coli BL21 (DE3)pLysS containing the NA gene of the H1N1 influenza virus produced this overexpressed enzyme in the insoluble fraction of cells in the form of inclusion bodies. The aim of this work was to investigate the effect of independent variables (propagation time, isopropyl β-d-1-thiogalactopyranoside (IPTG) concentration and expression time) on NA accumulation in inclusion bodies and to optimize these conditions by response surface methodology (RSM). The maximum yield of NA (112.97 ± 2.82 U/g) was achieved under optimal conditions, namely, a propagation time of 7.72 h, IPTG concentration of 1.82 mM and gene expression time of 7.35 h. This study demonstrated that bacterially expressed NA was enzymatically active.
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Affiliation(s)
- Sabina Lipničanová
- Department of Biotechnology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, J. Herdu 2, SK-91701 Trnava, Slovakia; (S.L.); (B.L.); (D.C.); (S.M.)
| | - Barbora Legerská
- Department of Biotechnology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, J. Herdu 2, SK-91701 Trnava, Slovakia; (S.L.); (B.L.); (D.C.); (S.M.)
| | - Daniela Chmelová
- Department of Biotechnology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, J. Herdu 2, SK-91701 Trnava, Slovakia; (S.L.); (B.L.); (D.C.); (S.M.)
| | - Miroslav Ondrejovič
- Department of Biotechnology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, J. Herdu 2, SK-91701 Trnava, Slovakia; (S.L.); (B.L.); (D.C.); (S.M.)
- International Centre for Applied Research and Sustainable Technology n.o., Jamnického 19, SK-84101 Bratislava, Slovakia
| | - Stanislav Miertuš
- Department of Biotechnology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, J. Herdu 2, SK-91701 Trnava, Slovakia; (S.L.); (B.L.); (D.C.); (S.M.)
- International Centre for Applied Research and Sustainable Technology n.o., Jamnického 19, SK-84101 Bratislava, Slovakia
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27
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Streamlining cell-free protein synthesis biosensors for use in human fluids: In situ RNase inhibitor production during extract preparation. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Different Regulatory Modes of Synechocystis sp. PCC 6803 in Response to Photosynthesis Inhibitory Conditions. mSystems 2021; 6:e0094321. [PMID: 34874777 PMCID: PMC8651088 DOI: 10.1128/msystems.00943-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Cyanobacteria are promising industrial platforms owing to their ability to produce diverse natural secondary metabolites and nonnative value-added biochemicals from CO2 and light. To fully utilize their industrial potency, it is critical to understand their photosynthetic efficiency under various environmental conditions. In this study, we elucidated the inhibitory mechanisms of photosynthesis under high-light and low-temperature stress conditions in the model cyanobacterium Synechocystis sp. PCC 6803. Under each stress condition, the transcript abundance and translation efficiency were measured using transcriptome sequencing (RNA-seq) and ribosome profiling, and the genome-wide transcription unit architecture was constructed by data integration of transcription start sites and transcript 3′-end positions obtained from differential RNA-seq and sequencing of 3′-ends (Term-seq), respectively. Our results suggested that the mode of photosynthesis inhibition differed between the two stress conditions; high light stress induced photodamage responses, while low temperature stress impaired the translation efficiency of photosynthesis-associated genes. In particular, poor translation of photosystem I resulted from ribosome stalling at the untranslated regions, affecting the overall photosynthetic yield under low temperature stress. Our comprehensive multiomics analysis with transcription unit architecture provides foundational information on photosynthesis for future industrial strain development. IMPORTANCE Cyanobacteria are a compelling biochemical production platform for their ability to propagate using light and atmospheric CO2 via photosynthesis. However, the engineering of strains is hampered by limited understanding of photosynthesis under diverse environmental conditions such as high-light and low-temperature stresses. Herein, we decipher the transcriptomic and translatomic responses of the photosynthetic efficiency to stress conditions using the integrative analysis of multiomic data generated by RNA-seq and ribosome profiling, respectively. Through the generated massive data, along with the guide of the genome-wide transcription unit architecture constructed by transcription start sites and transcript 3′-end positions, we identified the factors affecting photosynthesis at transcription, posttranscription, and translation levels. Importantly, the high-light stress induces photodamage responses, and the low-temperature stress cripples the translation efficiency of photosynthesis-associated genes. The resulting insights provide pivotal information for future cyanobacterial cell factories powered by the engineering toward robust photosynthesis ability.
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Perach M, Zafrir Z, Tuller T, Lewinson O. Identification of conserved slow codons that are important for protein expression and function. RNA Biol 2021; 18:2296-2307. [PMID: 33691590 PMCID: PMC8632084 DOI: 10.1080/15476286.2021.1901185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/28/2021] [Accepted: 03/06/2021] [Indexed: 10/21/2022] Open
Abstract
ABSTRASTDue to the redundancy of the genetic code most amino acids are encoded by several 'synonymous' codons. These codons are used unevenly, and each organism demonstrates its own unique codon usage bias, where the 'preferred' codons are associated with tRNAs that are found in high concentrations. Therefore, for decades, the prevailing view had been that preferred and non-preferred codons are linked to high or slow translation rates, respectively.However, this simplified view is contrasted by the frequent failures of codon-optimization efforts and by evidence of non-preferred (i.e. 'slow') codons having specific roles important for efficient production of functional proteins. One such specific role of slower codons is the regulation of co-translational protein folding, a complex biophysical process that is very challenging to model or to measure.Here, we combined a genome-wide approach with experiments to investigate the role of slow codons in protein production and co-translational folding. We analysed homologous gene groups from divergent bacteria and identified positions of inter-species conservation of bias towards slow codons. We then generated mutants where the conserved slow codons are substituted with 'fast' ones, and experimentally studied the effects of these codon substitutions. Using cellular and biochemical approaches we find that at certain locations, slow-to-fast codon substitutions reduce protein expression, increase protein aggregation, and impair protein function.This report provides an approach for identifying functionally relevant regions with slower codons and demonstrates that such codons are important for protein expression and function.
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Affiliation(s)
- Michal Perach
- Department of Molecular Microbiology, the Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Zohar Zafrir
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Oded Lewinson
- Department of Molecular Microbiology, the Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
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30
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Ferdous S, Dopp JL, Reuel NF. Optimization of E. Coli Tip-Sonication for High-Yield Cell-Free Extract using Finite Element Modeling. AIChE J 2021; 67:e17389. [PMID: 35663841 PMCID: PMC9161774 DOI: 10.1002/aic.17389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/17/2021] [Indexed: 12/23/2022]
Abstract
Optimal tip sonication settings, namely tip position, input power, and pulse durations, are necessary for temperature sensitive procedures like preparation of viable cell extract. In this paper, the optimum tip immersion depth (20-30% height below the liquid surface) is estimated which ensures maximum mixing thereby enhancing thermal dissipation of local cavitation hotspots. A finite element (FE) heat transfer model is presented, validated experimentally with (R2 > 97%) and used to observe the effect of temperature rise on cell extract performance of E. coli BL21 DE3 star strain and estimate the temperature threshold. Relative yields in the top 10% are observed for solution temperatures maintained below 32°C; this reduces below 50% relative yield at temperatures above 47°C. A generalized workflow for direct simulation using the COMSOL code as well as master plots for estimation of sonication parameters (power input and pulse settings) is also presented.
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Affiliation(s)
- Sakib Ferdous
- Department of Chemical and Biological Engineering, Iowa State University
| | - Jared L. Dopp
- Department of Chemical and Biological Engineering, Iowa State University
| | - Nigel F. Reuel
- Department of Chemical and Biological Engineering, Iowa State University
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31
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Do the differences in egg contamination, penetration, and resistance against microorganisms among the hen genotypes exist? ANNALS OF ANIMAL SCIENCE 2021. [DOI: 10.2478/aoas-2021-0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The aim of this study was to evaluate and compare the impact of genotype and storage conditions (temperature and time) on microbiological contamination and eggshell quality. There were four genotypes of laying hens used, Czech golden spotted (CGS), Greenleg Partridge (GP), White Leghorn (WL) and commercial hybrid (CH) hens were included. After collection, the eggs were divided equally into five groups regarding the storage time (0, 14, 28 days) and temperature (5 and 20 °C). The microbiological analysis included counting of colonies forming units (CFU) of Escherichia coli (EC), Enterococcus (ENT) and total number of microorganisms (TNM) on eggshell surface, eggshell membranes and in thin albumen. The analysis of eggshell quality included the determination of eggshell proportion (SP), thickness (ST), strength (SST), index (SI) and surface (SS). Moreover, egg weight (EW) and egg weight loss (EWL) were determined. The significant effect of genotype was found in contamination of eggshell by EC, ENT and TNM, eggshell membranes by TNM and albumen by EC (all P ≤ 0.05). The significantly lowest contamination of eggshell from EC was in eggs from the WL hens (4.42 log CFU/eggshell), while from ENT was in eggs from the CGS hens (1.22 log CFU/eggshell) and from the WL hens (1.40 log CFU/eggshell). The lowest incidence of TNM was also detected in eggs from the WL hens (5.03 log CFU/eggshell). Statistically the lowest contamination of eggshell membranes by TNM was found in eggs from the WL (0.12 log CFU/eggshell membranes) and CH hens (0.15 log CFU/eggshell membranes). Regarding the effect of genotype, the GP (not detected) and WL (not detected) hens was in eggs with statistically the lowest occurrence of EC bacteria in albumen. Regarding the EW and eggshell quality, all the parameters were significantly affected by the genotype (P ≤ 0.0001). Also EWL was significantly (P ≤ 0.05) affected by genotype (after 14, 21 and 28 days of storage). There were found to be significant differences of microbial contamination of egg surface among observed hen genotypes. The penetration of selected microorganisms was also significant in contamination of eggshell membranes by TNM and in contamination of albumen by EC.
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Shafat Z, Hamza A, Islam A, Al-Dosari MS, Parvez MK, Parveen S. Structural exploration of Y-domain reveals its essentiality in HEV pathogenesis. Protein Expr Purif 2021; 187:105947. [PMID: 34314826 DOI: 10.1016/j.pep.2021.105947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/21/2021] [Indexed: 12/19/2022]
Abstract
Hepatitis E virus (HEV) is a major causative agent of hepatitis E infections across the globe. Although the essentiality of HEV nonstructural polyprotein (pORF1) putative Y-domain (Yd) has been established in viral pathogenesis, its structural-functional role remains elusive. The current research discusses the novel exploration on Yd protein expression, purification, biophysical characterization and structure-based docking analysis. The codon optimized synthetic gene and optimized expression parameters i.e., 5 h induction with 0.25 mM IPTG at 37 °C, resulted in efficient production of Yd protein (∼40 kDa) in E. coli BL21(DE3) cells. Majority of the recombinant Yd (rYd) protein expressed as inclusion bodies was solubilized in 0.5% N-lauroylsarcosine and purified using Ni-NTA chromatography. Circular dichroism (CD) and UV visible absorption spectroscopic studies on Yd revealed both secondary and tertiary structure stability in alkaline range (pH 8.0-10.0), suggesting correlation with its physiological activity. Thus, loss in structure at low pH perhaps play crucial role in cytoplasmic-membrane interaction. The biophysical data were in good agreement with in-silico structural analyses, which suggested mixed α/β fold, non-random and basic nature of Yd protein. Furthermore, due to Yd protein essentiality in HEV replication and pathogenesis, it was considered as a template for docking and drug-likeness analyses. The 3D modeling of Yd protein and structure-based screening and drug-likeness of inhibitory compounds, including established antiviral drugs led to the identification of top nine promising candidates. Nonetheless, in vitro studies on the predicted interaction of Yd with intracellular-membrane towards establishing replication-complexes as well as validations of the proposed therapeutic agents are warranted.
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Affiliation(s)
- Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Abu Hamza
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohammed S Al-Dosari
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
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Dou M, Lu C, Rao W. Bioinspired materials and technology for advanced cryopreservation. Trends Biotechnol 2021; 40:93-106. [PMID: 34238601 DOI: 10.1016/j.tibtech.2021.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/25/2022]
Abstract
Cryopreservation can help to meet the demand for biosamples of high medical value. However, it remains difficult to effectively cryopreserve some sensitive cells, tissues, and reproductive organs. A coordinated effort from the perspective of the whole frozen biological system is necessary to advance cryopreservation technology. Animals that survive in cold temperatures, such as hibernators and cold-tolerant insects, offer excellent natural models. Their anti-cold strategies, such as programmed suppression of metabolism and the synthesis of cryoprotectants (CPAs), warrant systematic study. Furthermore, the discovery and synthesis of metabolism-regulating and cryoprotective biomaterials, combined with biotechnological breakthroughs, can also promote the development of cryopreservation. Further advances in the quality and duration of biosample storage inspired by nature will promote the application of cryopreserved biosamples in clinical therapy.
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Affiliation(s)
- Mengjia Dou
- Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; School of Engineering Science, University of Chinese Academy of Sciences, Beijing, 100049, China; Beijing Key Laboratory of Cryo-Biomedical Engineering, Beijing, 100190, China
| | - Chennan Lu
- Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; Beijing Key Laboratory of Cryo-Biomedical Engineering, Beijing, 100190, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Rao
- Key Laboratory of Cryogenics, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; Beijing Key Laboratory of Cryo-Biomedical Engineering, Beijing, 100190, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
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34
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Joseph TP, Zhao Q, Chanda W, Kanwal S, Fang Y, Zhong M, Huang M. Expression and in vitro anticancer activity of Lp16-PSP, a member of the YjgF/YER057c/UK114 protein family from the mushroom Lentinula edodes C 91-3. Arch Microbiol 2021; 203:1047-1060. [PMID: 33136174 DOI: 10.1007/s00203-020-02099-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 10/02/2020] [Accepted: 10/19/2020] [Indexed: 02/05/2023]
Abstract
Latcripin-16 (Lp16-PSP) is a gene that was extracted as a result of de novo characterization of the Lentinula edodes strain C91-3 transcriptome. The aim of the present study was to clone, express, and investigate the selective in vitro anticancer potential of Lp16-PSP in human cell lines. Lp16-PSP was analyzed using bioinformatics tools, cloned in a prokaryotic expression vector pET32a (+) and transformed into E. coli Rosetta gami. It was expressed and solubilized under optimized conditions. The differential scanning fluorometry (DSF)-guided refolding method was used with modifications to identify the proper refolding conditions for the Lp16-PSP protein. To determine the selective anticancer potential of Lp16-PSP, a panel of human cancerous and non-cancerous cell lines was used. Lp16-PSP protein was identified as endoribonuclease L-PSP protein and a member of the highly conserved YjgF/YER057c/UK114 protein superfamily. Lp16-PSP was expressed under optimized conditions (37 °C for 4 h following induction with 0.5 mM isopropyl β-D-1-thiogalactopyranoside). Solubilization was achieved with mild solubilization buffer containing 2 M urea using the freeze-thaw method. The DSF guided refolding method identified the proper refolding conditions (50 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA, 400 mM Arginine, 0.2 mM GSH and 2 mM GSSG; pH 8.0) for Lp16-PSP, with a melting transition of ~ 58 °C. A final yield of ~ 16 mg of purified Lp16-PSP from 1 L of culture was obtained following dialysis and concentration by PEG 20,000. A Cell Counting Kit-8 assay revealed the selective cytotoxic effect of Lp16-PSP. The HL-60 cell line was demonstrated to be most sensitive to Lp16-PSP, with an IC50 value of 74.4 ± 1.07 µg/ml. The results of the present study suggest that Lp16-PSP may serve as a potential anticancer agent; however, further investigation is required to characterize this anticancer effect and to elucidate the molecular mechanism underlying the action of Lp16-PSP.
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Affiliation(s)
- Thomson Patrick Joseph
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, 9 West Section, Lvshun South Road, Luvshoukon District, Dalian, 116044, Liaoning, People's Republic of China
- Center for Neuroscience, Shantou University Medical College, Shantou, People's Republic of China
| | - Qianqian Zhao
- Computational System Biology Laboratory, Department of Bioinformatics, Shantou University Medical College, Shantou, People's Republic of China
| | - Warren Chanda
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, 9 West Section, Lvshun South Road, Luvshoukon District, Dalian, 116044, Liaoning, People's Republic of China
| | - Sadia Kanwal
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Yukun Fang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, 9 West Section, Lvshun South Road, Luvshoukon District, Dalian, 116044, Liaoning, People's Republic of China
| | - MinTao Zhong
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, 9 West Section, Lvshun South Road, Luvshoukon District, Dalian, 116044, Liaoning, People's Republic of China
| | - Min Huang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, 9 West Section, Lvshun South Road, Luvshoukon District, Dalian, 116044, Liaoning, People's Republic of China.
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35
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Mairet F, Gouzé JL, de Jong H. Optimal proteome allocation and the temperature dependence of microbial growth laws. NPJ Syst Biol Appl 2021; 7:14. [PMID: 33686098 PMCID: PMC7940435 DOI: 10.1038/s41540-021-00172-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 01/15/2021] [Indexed: 11/14/2022] Open
Abstract
Although the effect of temperature on microbial growth has been widely studied, the role of proteome allocation in bringing about temperature-induced changes remains elusive. To tackle this problem, we propose a coarse-grained model of microbial growth, including the processes of temperature-sensitive protein unfolding and chaperone-assisted (re)folding. We determine the proteome sector allocation that maximizes balanced growth rate as a function of nutrient limitation and temperature. Calibrated with quantitative proteomic data for Escherichia coli, the model allows us to clarify general principles of temperature-dependent proteome allocation and formulate generalized growth laws. The same activation energy for metabolic enzymes and ribosomes leads to an Arrhenius increase in growth rate at constant proteome composition over a large range of temperatures, whereas at extreme temperatures resources are diverted away from growth to chaperone-mediated stress responses. Our approach points at risks and possible remedies for the use of ribosome content to characterize complex ecosystems with temperature variation.
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Affiliation(s)
- Francis Mairet
- Ifremer, Physiology and Biotechnology of Algae laboratory, Nantes, France.
| | - Jean-Luc Gouzé
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France
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36
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Shukla V, Phulara SC. Impact of culture condition modulation on the high-yield, high-specificity and cost-effective production of terpenoids from microbial sources: A review. Appl Environ Microbiol 2021; 87:AEM.02369-20. [PMID: 33257314 PMCID: PMC7851692 DOI: 10.1128/aem.02369-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent years have seen a remarkable increase in the non-natural production of terpenoids from microbial route. This is due to the advancements in synthetic biology tools and techniques, which have overcome the challenges associated with the non-native production of terpenoids from microbial hosts. Although, microbes in their native form have ability to grow in wide range of physicochemical parameters such as, pH, temperature, agitation, aeration etc; however, after genetic modifications, culture conditions need to be optimized in order to achieve improved titers of desired terpenoids from engineered microbes. The physicochemical parameters together with medium supplements, such as, inducer, carbon and nitrogen source, and cofactor supply not only play an important role in high-yield production of target terpenoids from engineered host, but also reduce the accumulation of undesired metabolites in fermentation medium, thus facilitate product recovery. Further, for the economic production of terpenoids, the biomass derived sugars can be utilized together with the optimized culture conditions. In the present mini-review, we have highlighted the impact of culture conditions modulation on the high-yield and high-specificity production of terpenoids from engineered microbes. Lastly, utilization of economic feedstock has also been discussed for the cost-effective and sustainable production of terpenoids.
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Affiliation(s)
- Vibha Shukla
- Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow-226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Suresh Chandra Phulara
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur-522502, Andhra Pradesh, India
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37
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Jiang W, Zeng W. Construction of a Self-Purification and Self-Assembly Coenzyme Regeneration System for the Synthesis of Chiral Drug Intermediates. ACS OMEGA 2021; 6:1911-1916. [PMID: 33521431 PMCID: PMC7841785 DOI: 10.1021/acsomega.0c04668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
As one of the important research contents of synthetic biology, the construction of a regulatory system exhibits great potential in the synthesis of high value-added chemicals such as drug intermediates. In this work, a self-assembly coenzyme regeneration system, leucine dehydrogenase (LeuDH)-formate dehydrogenase (FDH) protein co-assembly system, was constructed by using the polypeptide, SpyTag/SpyCatcher. Then, it was demonstrated that the nonchromatographic inverse transition cycling purification method could purify intracellular coupling proteins and extracellular coupling proteins well. The conversion rate of the pure LeuDH-FDH protein assembly (FR-LR) was shown to be 1.6-fold and 32.3-fold higher than that of the free LeuDH-FDH system (LeuDH + FDH) and free LeuDH, respectively. This work has paved a new way of constructing a protein self-assembly system and engineering self-purification coenzyme regeneration system for the synthesis of chiral amino acids or chiral α-hydroxy acids.
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Affiliation(s)
- Wei Jiang
- ; . Tel.: +86-05926162305. Fax: +86-05926162305
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38
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The impact of technical failures on recombinant production of soluble proteins in Escherichia coli: a case study on process and protein robustness. Bioprocess Biosyst Eng 2021; 44:1049-1061. [PMID: 33491129 PMCID: PMC8144139 DOI: 10.1007/s00449-021-02514-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 11/26/2020] [Indexed: 11/09/2022]
Abstract
Technical failures lead to deviations in process parameters that can exceed studied process boundaries. The impact on cell and target protein is often unknown. However, investigations on common technical failures might yield interesting insights into process and protein robustness. Recently, we published a study on the impact of technical failures on an inclusion body process that showed high robustness due to the inherent stability of IBs. In this follow-up study, we investigated the influence of technical failures during production of two soluble, cytosolic proteins in E. coli BL21(DE3). Cell physiology, productivity and protein quality were analyzed, after technical failures in aeration, substrate supply, temperature and pH control had been triggered. In most cases, cell physiology and productivity recovered during a subsequent regeneration phase. However, our results highlight that some technical failures lead to persistent deviations and affect the quality of purified protein.
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Elser JJ, Wu C, González AL, Shain DH, Smith HJ, Sommaruga R, Williamson CE, Brahney J, Hotaling S, Vanderwall J, Yu J, Aizen V, Aizen E, Battin TJ, Camassa R, Feng X, Jiang H, Lu L, Qu JJ, Ren Z, Wen J, Wen L, Woods HA, Xiong X, Xu J, Yu G, Harper JT, Saros JE. Key rules of life and the fading cryosphere: Impacts in alpine lakes and streams. GLOBAL CHANGE BIOLOGY 2020; 26:6644-6656. [PMID: 32969121 DOI: 10.1111/gcb.15362] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/07/2020] [Accepted: 08/30/2020] [Indexed: 06/11/2023]
Abstract
Alpine regions are changing rapidly due to loss of snow and ice in response to ongoing climate change. While studies have documented ecological responses in alpine lakes and streams to these changes, our ability to predict such outcomes is limited. We propose that the application of fundamental rules of life can help develop necessary predictive frameworks. We focus on four key rules of life and their interactions: the temperature dependence of biotic processes from enzymes to evolution; the wavelength dependence of the effects of solar radiation on biological and ecological processes; the ramifications of the non-arbitrary elemental stoichiometry of life; and maximization of limiting resource use efficiency across scales. As the cryosphere melts and thaws, alpine lakes and streams will experience major changes in temperature regimes, absolute and relative inputs of solar radiation in ultraviolet and photosynthetically active radiation, and relative supplies of resources (e.g., carbon, nitrogen, and phosphorus), leading to nonlinear and interactive effects on particular biota, as well as on community and ecosystem properties. We propose that applying these key rules of life to cryosphere-influenced ecosystems will reduce uncertainties about the impacts of global change and help develop an integrated global view of rapidly changing alpine environments. However, doing so will require intensive interdisciplinary collaboration and international cooperation. More broadly, the alpine cryosphere is an example of a system where improving our understanding of mechanistic underpinnings of living systems might transform our ability to predict and mitigate the impacts of ongoing global change across the daunting scope of diversity in Earth's biota and environments.
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Affiliation(s)
- James J Elser
- Flathead Lake Biological Station, University of Montana, Polson, MT, USA
| | - Chenxi Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Angélica L González
- Department of Biology & Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Daniel H Shain
- Department of Biology & Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Ruben Sommaruga
- Lake and Glacier Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | | | - Janice Brahney
- Department of Watershed Sciences, Utah State University, Logan, UT, USA
| | - Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Joseph Vanderwall
- Flathead Lake Biological Station, University of Montana, Polson, MT, USA
| | - Jinlei Yu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Science, Nanjing, China
| | - Vladimir Aizen
- Department of Geography, University of Idaho, Moscow, ID, USA
| | - Elena Aizen
- Department of Geography, University of Idaho, Moscow, ID, USA
| | - Tom J Battin
- Stream Biofilm and Ecosystem Research Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland
| | - Roberto Camassa
- Department of Mathematics, Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina, Chapel Hill, NC, USA
| | - Xiu Feng
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hongchen Jiang
- State Key Lab of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Lixin Lu
- Cooperative Institute for Research in the Atmosphere, Colorado State University, Fort Collins, CO, USA
| | - John J Qu
- Global Environment and Natural Resources Institute (GENRI) and Department of Geography and GeoInformation Science (GGS), George Mason University, Fairfax, VA, USA
| | - Ze Ren
- Flathead Lake Biological Station, University of Montana, Polson, MT, USA
| | - Jun Wen
- Sichuan Key Laboratory of Plateau Atmosphere and Environment, College of Atmospheric Sciences, Chengdu University of Information Technology, Chendu, China
| | - Lijuan Wen
- Key Laboratory of Land Surface Process and Climate Change in Cold and Arid Region, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - H Arthur Woods
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Xiong Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jun Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Gongliang Yu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Joel T Harper
- Department of Geosciences, University of Montana, Missoula, MT, USA
| | - Jasmine E Saros
- School of Biology and Ecology, Climate Change Institute, University of Maine, Orono, ME, USA
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40
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Knapp BD, Zhu L, Huang KC. SiCTeC: An inexpensive, easily assembled Peltier device for rapid temperature shifting during single-cell imaging. PLoS Biol 2020; 18:e3000786. [PMID: 33156840 PMCID: PMC7685484 DOI: 10.1371/journal.pbio.3000786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 11/24/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
Single-cell imaging, combined with recent advances in image analysis and microfluidic technologies, have enabled fundamental discoveries of cellular responses to chemical perturbations that are often obscured by traditional liquid-culture experiments. Temperature is an environmental variable well known to impact growth and to elicit specific stress responses at extreme values; it is often used as a genetic tool to interrogate essential genes. However, the dynamic effects of temperature shifts have remained mostly unstudied at the single-cell level, due largely to engineering challenges related to sample stability, heatsink considerations, and temperature measurement and feedback. Additionally, the few commercially available temperature-control platforms are costly. Here, we report an inexpensive (<$110) and modular Single-Cell Temperature Controller (SiCTeC) device for microbial imaging-based on straightforward modifications of the typical slide-sample-coverslip approach to microbial imaging-that controls temperature using a ring-shaped Peltier module and microcontroller feedback. Through stable and precise (±0.15°C) temperature control, SiCTeC achieves reproducible and fast (1-2 min) temperature transitions with programmable waveforms between room temperature and 45°C with an air objective. At the device's maximum temperature of 89°C, SiCTeC revealed that Escherichia coli cells progressively shrink and lose cellular contents. During oscillations between 30°C and 37°C, cells rapidly adapted their response to temperature upshifts. Furthermore, SiCTeC enabled the discovery of rapid morphological changes and enhanced sensitivity to substrate stiffness during upshifts to nonpermissive temperatures in temperature-sensitive mutants of cell-wall synthesis enzymes. Overall, the simplicity and affordability of SiCTeC empowers future studies of the temperature dependence of single-cell physiology.
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Affiliation(s)
- Benjamin D. Knapp
- Biophysics Program, Stanford University, Stanford, California, United States of America
| | - Lillian Zhu
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Kerwyn Casey Huang
- Biophysics Program, Stanford University, Stanford, California, United States of America
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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41
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Chang RL, Stanley JA, Robinson MC, Sher JW, Li Z, Chan YA, Omdahl AR, Wattiez R, Godzik A, Matallana-Surget S. Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage. EMBO J 2020; 39:e104523. [PMID: 33073387 PMCID: PMC7705453 DOI: 10.15252/embj.2020104523] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 02/05/2023] Open
Abstract
Oxidative stress alters cell viability, from microorganism irradiation sensitivity to human aging and neurodegeneration. Deleterious effects of protein carbonylation by reactive oxygen species (ROS) make understanding molecular properties determining ROS susceptibility essential. The radiation‐resistant bacterium Deinococcus radiodurans accumulates less carbonylation than sensitive organisms, making it a key model for deciphering properties governing oxidative stress resistance. We integrated shotgun redox proteomics, structural systems biology, and machine learning to resolve properties determining protein damage by γ‐irradiation in Escherichia coli and D. radiodurans at multiple scales. Local accessibility, charge, and lysine enrichment accurately predict ROS susceptibility. Lysine, methionine, and cysteine usage also contribute to ROS resistance of the D. radiodurans proteome. Our model predicts proteome maintenance machinery, and proteins protecting against ROS are more resistant in D. radiodurans. Our findings substantiate that protein‐intrinsic protection impacts oxidative stress resistance, identifying causal molecular properties.
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Affiliation(s)
- Roger L Chang
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Julian A Stanley
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Matthew C Robinson
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Joel W Sher
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Zhanwen Li
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Yujia A Chan
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Ashton R Omdahl
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Adam Godzik
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
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42
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Kastenhofer J, Rettenbacher L, Feuchtenhofer L, Mairhofer J, Spadiut O. Inhibition of E. coli Host RNA Polymerase Allows Efficient Extracellular Recombinant Protein Production by Enhancing Outer Membrane Leakiness. Biotechnol J 2020; 16:e2000274. [PMID: 32915502 DOI: 10.1002/biot.202000274] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/27/2020] [Indexed: 12/20/2022]
Abstract
With the growing interest in continuous cultivation of Escherichia coli, secretion of product to the medium is not only a benefit, but a necessity in future bioprocessing. In this study, it is shown that induced decoupling of growth and heterologous gene expression in the E. coli X-press strain (derived from BL21(DE3)) facilitates extracellular recombinant protein production. The effect of the process parameters temperature and specific glucose consumption rate (qS ) on growth, productivity, lysis and leakiness, is investigated, to find the parameter space allowing extracellular protein production. Two model proteins are used, Protein A (SpA) and a heavy-chain single-domain antibody (VHH), and performance is compared to the industrial standard strain BL21(DE3). It is shown that inducible growth repression in the X-press strain greatly mitigates the effect of metabolic burden under different process conditions. Furthermore, temperature and qS are used to control productivity and leakiness. In the X-press strain, extracellular SpA and VHH titer reach up to 349 and 19.6 mg g-1 , respectively, comprising up to 90% of the total soluble product, while keeping cell lysis at a minimum. The findings demonstrate that the X-press strain constitutes a valuable host for extracellular production of recombinant protein with E. coli.
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Affiliation(s)
- Jens Kastenhofer
- TU Wien, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Gumpendorfer Strasse 1a, Vienna, 1060, Austria
| | - Lukas Rettenbacher
- TU Wien, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Gumpendorfer Strasse 1a, Vienna, 1060, Austria
| | | | | | - Oliver Spadiut
- TU Wien, Environmental and Bioscience Engineering, Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Gumpendorfer Strasse 1a, Vienna, 1060, Austria
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43
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The effect of transport temperature and time on the recovery of antimicrobial-resistant Enterobacterales in stool. Diagn Microbiol Infect Dis 2020; 99:115210. [PMID: 33242837 DOI: 10.1016/j.diagmicrobio.2020.115210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/10/2020] [Accepted: 09/10/2020] [Indexed: 02/01/2023]
Abstract
Surveillance for antibiotic-resistant (AR) bacteria is challenging. We evaluated AR Enterobacterales survival in stool over various transport conditions. Stool in Cary-Blair medium was spiked with AR Enterobacterales, held at 3 °C, 20 °C, or 37 °C, and cultured on days 3, 8, and 15. Stool from US international travelers sent through the US mail was also screened. We compared recovery rates using Fisher's exact tests and linear regression models. AR Enterobacterales recovery reduced with time (86% versus 75% versus 61% at days 3, 8, and 15; Beta for linear trend=-0.02, r2=0.99, P=0.02) and colder temperatures [56% (3 °C) versus 89% (20 °C) versus 86% (37 °C); P=0.003]. Traveler sample recovery also reduced with transport time (Beta for linear trend=-0.03, r2=0.70, P=0.01) but not with season [20% (cold) versus 22% (warm), P=0.7]. AR Enterobacterales are found over variable transport conditions, providing rationale for expanding surveillance sample processing timelines.
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44
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Efficiency and Robustness of Processes Driven by Nucleoid Exclusion in Escherichia coli. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020. [PMID: 32894477 DOI: 10.1007/978-3-030-46886-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The internal spatial organization of prokaryotic organisms, including Escherichia coli, is essential for the proper functioning of processes such as cell division. One source of this organization in E. coli is the nucleoid, which causes the exclusion of macromolecules - e.g. protein aggregates and the chemotaxis network - from midcell. Similarly, following DNA replication, the nucleoid(s) assist in placing the Z-ring at midcell. These processes need to be efficient in optimal conditions and robust to suboptimal conditions. After reviewing recent findings on these topics, we make use of past data to study the efficiency of the spatial constraining of Z-rings, chemotaxis networks, and protein aggregates, as a function of the nucleoid(s) morphology. Also, we compare the robustness of these processes to nonoptimal temperatures. We show that Z-rings, Tsr clusters, and protein aggregates have temperature-dependent spatial distributions along the major cell axis that are consistent with the nucleoid(s) morphology and the volume-exclusion phenomenon. Surprisingly, the consequences of the changes in nucleoid size with temperature are most visible in the kurtosis of these spatial distributions, in that it has a statistically significant linear correlation with the mean nucleoid length and, in the case of Z-rings, with the distance between nucleoids prior to cell division. Interestingly, we also find a negative, statistically significant linear correlation between the efficiency of these processes at the optimal condition and their robustness to suboptimal conditions, suggesting a trade-off between these traits.
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45
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Control of ribosome synthesis in bacteria: the important role of rRNA chain elongation rate. SCIENCE CHINA-LIFE SCIENCES 2020; 64:795-802. [DOI: 10.1007/s11427-020-1742-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/26/2020] [Indexed: 10/23/2022]
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46
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Colant N, Melinek B, Teneb J, Goldrick S, Rosenberg W, Frank S, Bracewell DG. A rational approach to improving titer in Escherichia coli-based cell-free protein synthesis reactions. Biotechnol Prog 2020; 37:e3062. [PMID: 32761750 DOI: 10.1002/btpr.3062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/14/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023]
Abstract
Cell-free protein synthesis (CFPS) is an established method for rapid recombinant protein production. Advantages like short synthesis times and an open reaction environment make CFPS a desirable platform for new and difficult-to-express products. Most recently, interest has grown in using the technology to make larger amounts of material. This has been driven through a variety of reasons from making site specific antibody drug conjugates, to emergency response, to the safe manufacture of toxic biological products. We therefore need robust methods to determine the appropriate reaction conditions for product expression in CFPS. Here we propose a process development strategy for Escherichia coli lysate-based CFPS reactions that can be completed in as little as 48 hr. We observed the most dramatic increases in titer were due to the E. coli strain for the cell extract. Therefore, we recommend identifying a high-producing cell extract for the product of interest as a first step. Next, we manipulated the plasmid concentration, amount of extract, temperature, concentrated reaction mix pH levels, and length of reaction. The influence of these process parameters on titer was evaluated through multivariate data analysis. The process parameters with the highest impact on titer were subsequently included in a design of experiments to determine the conditions that increased titer the most in the design space. This proposed process development strategy resulted in superfolder green fluorescent protein titers of 0.686 g/L, a 38% improvement on the standard operating conditions, and hepatitis B core antigen titers of 0.386 g/L, a 190% improvement.
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Affiliation(s)
- Noelle Colant
- Department of Biochemical Engineering, University College London, London, UK
| | - Beatrice Melinek
- Department of Biochemical Engineering, University College London, London, UK
| | - Jaime Teneb
- Department of Biochemical Engineering, University College London, London, UK
| | - Stephen Goldrick
- Department of Biochemical Engineering, University College London, London, UK
| | - William Rosenberg
- UCL Institute for Liver and Digestive Health, Division of Medicine, Royal Free Campus, London, UK
| | - Stefanie Frank
- Department of Biochemical Engineering, University College London, London, UK
| | - Daniel G Bracewell
- Department of Biochemical Engineering, University College London, London, UK
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47
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Dai X, Zhu M. Coupling of Ribosome Synthesis and Translational Capacity with Cell Growth. Trends Biochem Sci 2020; 45:681-692. [DOI: 10.1016/j.tibs.2020.04.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/11/2020] [Accepted: 04/27/2020] [Indexed: 12/31/2022]
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48
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Abstract
Antibiotics constitute one of the cornerstones of modern medicine. However, individuals may succumb to a bacterial infection if a pathogen survives exposure to antibiotics. The ability of bacteria to survive bactericidal antibiotics results from genetic changes in the preexisting bacterial genome, from the acquisition of genes from other organisms, and from nonheritable phenomena that give rise to antibiotic tolerance. Nonheritable antibiotic tolerance can be exhibited by a large fraction of the bacterial population or by a small subpopulation referred to as persisters. Nonheritable resistance to antibiotics has been ascribed to the activity of toxins that are part of toxin-antitoxin modules, to the universal energy currency ATP, and to the signaling molecule guanosine (penta) tetraphosphate. However, these molecules are dispensable for nonheritable resistance to antibiotics in many organisms. By contrast, nutrient limitation, treatment with bacteriostatic antibiotics, or expression of genes that slow bacterial growth invariably promote nonheritable resistance. We posit that antibiotic persistence results from conditions promoting feedback inhibition among core cellular processes, resulting phenotypically in a slowdown or halt in bacterial growth.
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49
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Hossain MT, Yokono T, Kashiwagi A. The Single-Stranded RNA Bacteriophage Qβ Adapts Rapidly to High Temperatures: An Evolution Experiment. Viruses 2020; 12:v12060638. [PMID: 32545482 PMCID: PMC7354602 DOI: 10.3390/v12060638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 11/22/2022] Open
Abstract
Single-stranded (ss)RNA viruses are thought to evolve rapidly due to an inherently high mutation rate. However, it remains unclear how ssRNA viruses adapt to novel environments and/or how many and what types of substitutions are needed to facilitate this evolution. In this study, we followed the adaptation of the ssRNA bacteriophage Qβ using thermally adapted Escherichia coli as a host, which can efficiently grow at temperatures between 37.2 and 45.3 °C. This made it possible to evaluate Qβ adaptation to the highest known temperature that supports growth, 45.3 °C. We found that Qβ was capable of replication at this temperature; within 114 days (~1260 generations), we detected more than 34 novel point mutations in the genome of the thermally adapted Qβ population, representing 0.8% of the total Qβ genome. In addition, we returned the 45.3 °C-adapted Qβ populations to 37.2 °C and passaged them for 8 days (~124 generations). We found that the reverse-adapted Qβ population showed little to no decrease in fitness. These results indicate that Qβ can evolve in response to increasing temperatures in a short period of time with the accumulation of point mutations.
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Affiliation(s)
- Md. Tanvir Hossain
- The United Graduate School of Agricultural Science, Iwate University, Morioka 020-8550, Japan;
| | - Toma Yokono
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan;
| | - Akiko Kashiwagi
- The United Graduate School of Agricultural Science, Iwate University, Morioka 020-8550, Japan;
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan;
- Correspondence: ; Tel.: +81-172-39-3789
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Combined Optimization of Codon Usage and Glycine Supplementation Enhances the Extracellular Production of a β-Cyclodextrin Glycosyltransferase from Bacillus sp. NR5 UPM in Escherichia coli. Int J Mol Sci 2020; 21:ijms21113919. [PMID: 32486212 PMCID: PMC7313058 DOI: 10.3390/ijms21113919] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 11/24/2022] Open
Abstract
Two optimization strategies, codon usage modification and glycine supplementation, were adopted to improve the extracellular production of Bacillus sp. NR5 UPM β-cyclodextrin glycosyltransferase (CGT-BS) in recombinant Escherichia coli. Several rare codons were eliminated and replaced with the ones favored by E. coli cells, resulting in an increased codon adaptation index (CAI) from 0.67 to 0.78. The cultivation of the codon modified recombinant E. coli following optimization of glycine supplementation enhanced the secretion of β-CGTase activity up to 2.2-fold at 12 h of cultivation as compared to the control. β-CGTase secreted into the culture medium by the transformant reached 65.524 U/mL at post-induction temperature of 37 °C with addition of 1.2 mM glycine and induced at 2 h of cultivation. A 20.1-fold purity of the recombinant β-CGTase was obtained when purified through a combination of diafiltration and nickel-nitrilotriacetic acid (Ni-NTA) affinity chromatography. This combined strategy doubled the extracellular β-CGTase production when compared to the single approach, hence offering the potential of enhancing the expression of extracellular enzymes, particularly β-CGTase by the recombinant E. coli.
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