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Sayer AP, Llavero-Pasquina M, Geisler K, Holzer A, Bunbury F, Mendoza-Ochoa GI, Lawrence AD, Warren MJ, Mehrshahi P, Smith AG. Conserved cobalamin acquisition protein 1 is essential for vitamin B12 uptake in both Chlamydomonas and Phaeodactylum. Plant Physiol 2024; 194:698-714. [PMID: 37864825 PMCID: PMC10828217 DOI: 10.1093/plphys/kiad564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/01/2023] [Accepted: 08/18/2023] [Indexed: 10/23/2023]
Abstract
Microalgae play an essential role in global net primary productivity and global biogeochemical cycling. Despite their phototrophic lifestyle, over half of algal species depend for growth on acquiring an external supply of the corrinoid vitamin B12 (cobalamin), a micronutrient produced only by a subset of prokaryotic organisms. Previous studies have identified protein components involved in vitamin B12 uptake in bacterial species and humans. However, little is known about its uptake in algae. Here, we demonstrate the essential role of a protein, cobalamin acquisition protein 1 (CBA1), in B12 uptake in Phaeodactylum tricornutum using CRISPR-Cas9 to generate targeted knockouts and in Chlamydomonas reinhardtii by insertional mutagenesis. In both cases, CBA1 knockout lines could not take up exogenous vitamin B12. Complementation of the C. reinhardtii mutants with the wild-type CBA1 gene restored B12 uptake, and regulation of CBA1 expression via a riboswitch element enabled control of the phenotype. When visualized by confocal microscopy, a YFP-fusion with C. reinhardtii CBA1 showed association with membranes. Bioinformatics analysis found that CBA1-like sequences are present in all major eukaryotic phyla. In algal taxa, the majority that encoded CBA1 also had genes for B12-dependent enzymes, suggesting CBA1 plays a conserved role. Our results thus provide insight into the molecular basis of algal B12 acquisition, a process that likely underpins many interactions in aquatic microbial communities.
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Affiliation(s)
- Andrew P Sayer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Marcel Llavero-Pasquina
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Katrin Geisler
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Freddy Bunbury
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Gonzalo I Mendoza-Ochoa
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Andrew D Lawrence
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UA, UK
| | - Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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Mehrshahi P, Nguyen GTDT, Gorchs Rovira A, Sayer A, Llavero-Pasquina M, Lim Huei Sin M, Medcalf EJ, Mendoza-Ochoa GI, Scaife MA, Smith AG. Development of Novel Riboswitches for Synthetic Biology in the Green Alga Chlamydomonas. ACS Synth Biol 2020; 9:1406-1417. [PMID: 32496044 PMCID: PMC7309327 DOI: 10.1021/acssynbio.0c00082] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Riboswitches are RNA regulatory elements that bind specific ligands to control gene expression. Because of their modular composition, where a ligand-sensing aptamer domain is combined with an expression platform, riboswitches offer unique tools for synthetic biology applications. Here we took a mutational approach to determine functionally important nucleotide residues in the thiamine pyrophosphate (TPP) riboswitch in the THI4 gene of the model alga Chlamydomonas reinhardtii, allowing us to carry out aptamer swap using THIC aptamers from Chlamydomonas and Arabidopsis thaliana. These chimeric riboswitches displayed a distinct specificity and dynamic range of responses to different ligands. Our studies demonstrate ease of assembly as 5'UTR DNA parts, predictability of output, and utility for controlled production of a high-value compound in Chlamydomonas. The simplicity of riboswitch incorporation in current design platforms will facilitate the generation of genetic circuits to advance synthetic biology and metabolic engineering of microalgae.
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Affiliation(s)
- Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Ginnie Trinh D. T. Nguyen
- Glanbia Performance Nutrition Canada Inc., 3500 Lacey Road, Suite 1200, Downers Grove, Illinois 60515, United States
| | - Aleix Gorchs Rovira
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Andrew Sayer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Marcel Llavero-Pasquina
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Michelle Lim Huei Sin
- John Swire & Sons (H.K.) Ltd. 33/F One Pacific Place, 88 Queensway, Hong Kong, China
| | - Elliot J. Medcalf
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | | | - Mark A. Scaife
- Mara Renewables Corporation, 101A Research Drive, Dartmouth, Nova Scotia B2Y 4T6, Canada
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
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Abstract
Pre-messenger RNA splicing involves multi-step assembly of the large spliceosome complexes that catalyse the two consecutive trans-esterification reactions, resulting in intron removal. There is evidence that proof-reading mechanisms monitor the fidelity of this complex process. Transcripts that fail these fidelity tests are thought to be directed to degradation pathways, permitting the splicing factors to be recycled. While studying the roles of splicing factors in vivo, in budding yeast, we performed targeted depletion of individual proteins, and analysed the effect on co-transcriptional spliceosome assembly and splicing efficiency. Unexpectedly, depleting factors such as Prp16 or Prp22, that are known to function at the second catalytic step or later in the splicing pathway, resulted in a defect in the first step of splicing, and accumulation of arrested spliceosomes. Through a kinetic analysis of newly synthesized RNA, we observed that a second step splicing defect (the primary defect) was rapidly followed by the first step of splicing defect. Our results show that knocking down a splicing factor can quickly lead to a recycling defect with splicing factors sequestered in stalled complexes, thereby limiting new rounds of splicing. We demonstrate that this ‘feed-back’ effect can be minimized by depleting the target protein more gradually or only partially, allowing a better separation between primary and secondary effects. Our findings indicate that splicing surveillance mechanisms may not always cope with spliceosome assembly defects, and suggest that work involving knock-down of splicing factors or components of other large complexes should be carefully monitored to avoid potentially misleading conclusions.
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Affiliation(s)
- Gonzalo I Mendoza-Ochoa
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J David Barrass
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Isabella E Maudlin
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jean D Beggs
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Barrass JD, Mendoza-Ochoa GI, Maudlin IE, Sani E, Beggs JD. Tuning Degradation to Achieve Specific and Efficient Protein Depletion. J Vis Exp 2019. [PMID: 31380835 DOI: 10.3791/59874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The plant auxin binding receptor, TIR1, recognizes proteins containing a specific auxin-inducible degron (AID) motif in the presence of auxin, targeting them for degradation. This system is exploited in many non-plant eukaryotes, such that a target protein, tagged with the AID motif, is degraded upon auxin addition. The level of TIR1 expression is critical; excessive expression leads to degradation of the AID-tagged protein even in the absence of auxin, whereas low expression leads to slow depletion. A β-estradiol-inducible AID system was created, with expression of TIR1 under the control of a β-estradiol inducible promoter. The level of TIR1 is tunable by changing the time of incubation with β-estradiol before auxin addition. This protocol describes how to rapidly deplete a target protein using the AID system. The appropriate β-estradiol incubation time depends on the abundance of the target protein. Therefore, efficient depletion depends on optimal timing that also minimizes auxin-independent depletion.
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Affiliation(s)
- J David Barrass
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh;
| | - Gonzalo I Mendoza-Ochoa
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Department of Plant Sciences, University of Cambridge
| | - Isabella E Maudlin
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Sir William Dunn School of Pathology, University of Oxford
| | - Emanuela Sani
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh
| | - Jean D Beggs
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh
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Mendoza-Ochoa GI, Barrass JD, Terlouw BR, Maudlin IE, de Lucas S, Sani E, Aslanzadeh V, Reid JAE, Beggs JD. A fast and tuneable auxin-inducible degron for depletion of target proteins in budding yeast. Yeast 2018; 36:75-81. [PMID: 30375036 PMCID: PMC6587778 DOI: 10.1002/yea.3362] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/02/2018] [Accepted: 10/16/2018] [Indexed: 12/11/2022] Open
Abstract
The auxin‐inducible degron (AID) is a useful technique to rapidly deplete proteins of interest in nonplant eukaryotes. Depletion is achieved by addition of the plant hormone auxin to the cell culture, which allows the auxin‐binding receptor, TIR1, to target the AID‐tagged protein for degradation by the proteasome. Fast depletion of the target protein requires good expression of TIR1 protein, but as we show here, high levels of TIR1 may cause uncontrolled depletion of the target protein in the absence of auxin. To enable conditional expression of TIR1 to a high level when required, we regulated the expression of TIR1 using the β‐estradiol expression system. This is a fast‐acting gene induction system that does not cause secondary effects on yeast cell metabolism. We demonstrate that combining the AID and β‐estradiol systems results in a tightly controlled and fast auxin‐induced depletion of nuclear target proteins. Moreover, we show that depletion rate can be tuned by modulating the duration of β‐estradiol preincubation. We conclude that TIR1 protein is a rate‐limiting factor for target protein depletion in yeast, and we provide new tools that allow tightly controlled, tuneable, and efficient depletion of essential proteins whereas minimising secondary effects.
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Affiliation(s)
- Gonzalo I Mendoza-Ochoa
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J David Barrass
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Barbara R Terlouw
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Isabella E Maudlin
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susana de Lucas
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Emanuela Sani
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Vahid Aslanzadeh
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jane A E Reid
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jean D Beggs
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Aguilar-Yáñez JM, Portillo-Lara R, Mendoza-Ochoa GI, García-Echauri SA, López-Pacheco F, Bulnes-Abundis D, Salgado-Gallegos J, Lara-Mayorga IM, Webb-Vargas Y, León-Angel FO, Rivero-Aranda RE, Oropeza-Almazán Y, Ruiz-Palacios GM, Zertuche-Guerra MI, DuBois RM, White SW, Schultz-Cherry S, Russell CJ, Alvarez MM. An influenza A/H1N1/2009 hemagglutinin vaccine produced in Escherichia coli. PLoS One 2010; 5:e11694. [PMID: 20661476 PMCID: PMC2908544 DOI: 10.1371/journal.pone.0011694] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 06/09/2010] [Indexed: 11/28/2022] Open
Abstract
Background The A/H1N1/2009 influenza pandemic made evident the need for faster and higher-yield methods for the production of influenza vaccines. Platforms based on virus culture in mammalian or insect cells are currently under investigation. Alternatively, expression of fragments of the hemagglutinin (HA) protein in prokaryotic systems can potentially be the most efficacious strategy for the manufacture of large quantities of influenza vaccine in a short period of time. Despite experimental evidence on the immunogenic potential of HA protein constructs expressed in bacteria, it is still generally accepted that glycosylation should be a requirement for vaccine efficacy. Methodology/Principal Findings We expressed the globular HA receptor binding domain, referred to here as HA63–286-RBD, of the influenza A/H1N1/2009 virus in Escherichia coli using a simple, robust and scalable process. The recombinant protein was refolded and purified from the insoluble fraction of the cellular lysate as a single species. Recombinant HA63–286-RBD appears to be properly folded, as shown by analytical ultracentrifugation and bio-recognition assays. It binds specifically to serum antibodies from influenza A/H1N1/2009 patients and was found to be immunogenic, to be capable of triggering the production of neutralizing antibodies, and to have protective activity in the ferret model. Conclusions/Significance Projections based on our production/purification data indicate that this strategy could yield up to half a billion doses of vaccine per month in a medium-scale pharmaceutical production facility equipped for bacterial culture. Also, our findings demonstrate that glycosylation is not a mandatory requirement for influenza vaccine efficacy.
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Affiliation(s)
- José M. Aguilar-Yáñez
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Monterrey, México
| | - Roberto Portillo-Lara
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Monterrey, México
| | | | | | - Felipe López-Pacheco
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Monterrey, México
| | - David Bulnes-Abundis
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Monterrey, México
| | | | - Itzel M. Lara-Mayorga
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Monterrey, México
| | - Yenny Webb-Vargas
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Monterrey, México
| | - Felipe O. León-Angel
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Monterrey, México
| | | | | | | | | | - Rebecca M. DuBois
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Stephen W. White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Charles J. Russell
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Mario M. Alvarez
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Monterrey, México
- * E-mail:
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Alvarez MM, López-Pacheco F, Aguilar-Yañez JM, Portillo-Lara R, Mendoza-Ochoa GI, García-Echauri S, Freiden P, Schultz-Cherry S, Zertuche-Guerra MI, Bulnes-Abundis D, Salgado-Gallegos J, Elizondo-Montemayor L, Hernández-Torre M. Specific recognition of influenza A/H1N1/2009 antibodies in human serum: a simple virus-free ELISA method. PLoS One 2010; 5:e10176. [PMID: 20418957 PMCID: PMC2854694 DOI: 10.1371/journal.pone.0010176] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 03/16/2010] [Indexed: 12/16/2022] Open
Abstract
Background Although it has been estimated that pandemic Influenza A H1N1/2009 has infected millions of people from April to October 2009, a more precise figure requires a worldwide large-scale diagnosis of the presence of Influenza A/H1N1/2009 antibodies within the population. Assays typically used to estimate antibody titers (hemagglutination inhibition and microneutralization) would require the use of the virus, which would seriously limit broad implementation. Methodology/Principal Findings An ELISA method to evaluate the presence and relative concentration of specific Influenza A/H1N1/2009 antibodies in human serum samples is presented. The method is based on the use of a histidine-tagged recombinant fragment of the globular region of the hemagglutinin (HA) of the Influenza A H1N1/2009 virus expressed in E. coli. Conclusions/Significance The ELISA method consistently discerns between Inf A H1N1 infected and non-infected subjects, particularly after the third week of infection/exposure. Since it does not require the use of viral particles, it can be easily and quickly implemented in any basic laboratory. In addition, in a scenario of insufficient vaccine availability, the use of this ELISA could be useful to determine if a person has some level of specific antibodies against the virus and presumably at least partial protection.
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Affiliation(s)
- Mario M Alvarez
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey, Monterrey, New León, México.
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