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Abstract
Genetic coding in bacteria largely operates via the "one gene-one protein" paradigm. However, the peculiarities of the mRNA structure, the versatility of the genetic code, and the dynamic nature of translation sometimes allow organisms to deviate from the standard rules of protein encoding. Bacteria can use several unorthodox modes of translation to express more than one protein from a single mRNA cistron. One such alternative path is the use of additional translation initiation sites within the gene. Proteins whose translation is initiated at different start sites within the same reading frame will differ in their N termini but will have identical C-terminal segments. On the other hand, alternative initiation of translation in a register different from the frame dictated by the primary start codon will yield a protein whose sequence is entirely different from the one encoded in the main frame. The use of internal mRNA codons as translation start sites is controlled by the nucleotide sequence and the mRNA folding. The proteins of the alternative proteome generated via the "genes-within-genes" strategy may carry important functions. In this review, we summarize the currently known examples of bacterial genes encoding more than one protein due to the utilization of additional translation start sites and discuss the known or proposed functions of the alternative polypeptides in relation to the main protein product of the gene. We also discuss recent proteome- and genome-wide approaches that will allow the discovery of novel translation initiation sites in a systematic fashion.
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152
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Sommer M, Sutter M, Gupta S, Kirst H, Turmo A, Lechno-Yossef S, Burton RL, Saechao C, Sloan NB, Cheng X, Chan LJG, Petzold CJ, Fuentes-Cabrera M, Ralston CY, Kerfeld CA. Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells. PLANT PHYSIOLOGY 2019; 179:156-167. [PMID: 30389783 PMCID: PMC6324227 DOI: 10.1104/pp.18.01190] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/26/2018] [Indexed: 05/10/2023]
Abstract
Bacterial microcompartments (BMCs) encapsulate enzymes within a selectively permeable, proteinaceous shell. Carboxysomes are BMCs containing ribulose-1,5-bisphosphate carboxylase oxygenase and carbonic anhydrase that enhance carbon dioxide fixation. The carboxysome shell consists of three structurally characterized protein types, each named after the oligomer they form: BMC-H (hexamer), BMC-P (pentamer), and BMC-T (trimer). These three protein types form cyclic homooligomers with pores at the center of symmetry that enable metabolite transport across the shell. Carboxysome shells contain multiple BMC-H paralogs, each with distinctly conserved residues surrounding the pore, which are assumed to be associated with specific metabolites. We studied the regulation of β-carboxysome shell composition by investigating the BMC-H genes ccmK3 and ccmK4 situated in a locus remote from other carboxysome genes. We made single and double deletion mutants of ccmK3 and ccmK4 in Synechococcus elongatus PCC7942 and show that, unlike CcmK3, CcmK4 is necessary for optimal growth. In contrast to other CcmK proteins, CcmK3 does not form homohexamers; instead CcmK3 forms heterohexamers with CcmK4 with a 1:2 stoichiometry. The CcmK3-CcmK4 heterohexamers form stacked dodecamers in a pH-dependent manner. Our results indicate that CcmK3-CcmK4 heterohexamers potentially expand the range of permeability properties of metabolite channels in carboxysome shells. Moreover, the observed facultative formation of dodecamers in solution suggests that carboxysome shell permeability may be dynamically attenuated by "capping" facet-embedded hexamers with a second hexamer. Because β-carboxysomes are obligately expressed, heterohexamer formation and capping could provide a rapid and reversible means to alter metabolite flux across the shell in response to environmental/growth conditions.
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Affiliation(s)
- Manuel Sommer
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Markus Sutter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Sayan Gupta
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Henning Kirst
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Aiko Turmo
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Sigal Lechno-Yossef
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Rodney L Burton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Christine Saechao
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Nancy B Sloan
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy and Biophysics Graduate Program, Ohio State University, Columbus, Ohio 43210
| | - Leanne-Jade G Chan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Miguel Fuentes-Cabrera
- Center for Nanophase Materials Sciences and Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennesse 37831
| | - Corie Y Ralston
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Cheryl A Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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153
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Ryan P, Forrester TJB, Wroblewski C, Kenney TMG, Kitova EN, Klassen JS, Kimber MS. The small RbcS-like domains of the β-carboxysome structural protein CcmM bind RubisCO at a site distinct from that binding the RbcS subunit. J Biol Chem 2018; 294:2593-2603. [PMID: 30591587 DOI: 10.1074/jbc.ra118.006330] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/13/2018] [Indexed: 12/26/2022] Open
Abstract
Carboxysomes are compartments in bacterial cells that promote efficient carbon fixation by sequestering RubisCO and carbonic anhydrase within a protein shell that impedes CO2 escape. The key to assembling this protein complex is CcmM, a multidomain protein whose C-terminal region is required for RubisCO recruitment. This CcmM region is built as a series of copies (generally 3-5) of a small domain, CcmMS, joined by unstructured linkers. CcmMS domains have weak, but significant, sequence identity to RubisCO's small subunit, RbcS, suggesting that CcmM binds RubisCO by displacing RbcS. We report here the 1.35-Å structure of the first Thermosynechococcus elongatus CcmMS domain, revealing that it adopts a compact, well-defined structure that resembles that of RbcS. CcmMS, however, lacked key RbcS RubisCO-binding determinants, most notably an extended N-terminal loop. Nevertheless, individual CcmMS domains are able to bind RubisCO in vitro with 1.16 μm affinity. Two or four linked CcmMS domains did not exhibit dramatic increases in this affinity, implying that short, disordered linkers may frustrate successive CcmMS domains attempting to simultaneously bind a single RubisCO oligomer. Size-exclusion chromatography-coupled right-angled light scattering (SEC-RALS) and native MS experiments indicated that multiple CcmMS domains can bind a single RubisCO holoenzyme and, moreover, that RbcS is not released from these complexes. CcmMS bound equally tightly to a RubisCO variant in which the α/β domain of RbcS was deleted, suggesting that CcmMS binds RubisCO independently of its RbcS subunit. We propose that, instead, the electropositive CcmMS may bind to an extended electronegative pocket between RbcL dimers.
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Affiliation(s)
- Patrick Ryan
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Taylor J B Forrester
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Charles Wroblewski
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Tristan M G Kenney
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Matthew S Kimber
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
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154
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MacCready JS, Hakim P, Young EJ, Hu L, Liu J, Osteryoung KW, Vecchiarelli AG, Ducat DC. Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria. eLife 2018; 7:39723. [PMID: 30520729 PMCID: PMC6328274 DOI: 10.7554/elife.39723] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/19/2018] [Indexed: 12/25/2022] Open
Abstract
Carboxysomes are protein-based bacterial organelles encapsulating key enzymes of the Calvin-Benson-Bassham cycle. Previous work has implicated a ParA-like protein (hereafter McdA) as important for spatially organizing carboxysomes along the longitudinal axis of the model cyanobacterium Synechococcus elongatus PCC 7942. Yet, how self-organization of McdA emerges and contributes to carboxysome positioning is unknown. Here, we identify a small protein, termed McdB that localizes to carboxysomes and drives emergent oscillatory patterning of McdA on the nucleoid. Our results demonstrate that McdB directly stimulates McdA ATPase activity and its release from DNA, driving carboxysome-dependent depletion of McdA locally on the nucleoid and promoting directed motion of carboxysomes towards increased concentrations of McdA. We propose that McdA and McdB are a previously unknown class of self-organizing proteins that utilize a Brownian-ratchet mechanism to position carboxysomes in cyanobacteria, rather than a cytoskeletal system. These results have broader implications for understanding spatial organization of protein mega-complexes and organelles in bacteria. Cyanobacteria are tiny organisms that can harness the energy of the sun to power their cells. Many of the tools required for this complex photosynthetic process are packaged into small compartments inside the cell, the carboxysomes. In Synechococcus elongatus, a cyanobacterium that is shaped like a rod, the carboxysomes are positioned at regular intervals along the length of the cell. This ensures that, when the bacterium splits itself in half to reproduce, both daughter cells have the same number of carboxysomes. Researchers know that, in S. elongatus, a protein called McdA can oscillate from one end of the cell to the other. This protein is responsible for the carboxysomes being in the right place, and some scientists believe that it helps to create an internal skeleton that anchors and drags the compartments into position. Here, MacCready et al. propose another mechanism and, by combining various approaches, identify a new partner for McdA. This protein, called McdB, is present on the carboxysomes. McdB also binds to McdA, which itself attaches to the nucleoid – the region in the cell that contains the DNA. McdB forces McdA to release itself from DNA, causing the protein to reposition itself along the nucleoid. Because McdB attaches to McdA, the carboxysomes then follow suit, constantly seeking the highest concentrations of McdA bound to nearby DNA. Instead of relying on a cellular skeleton, these two proteins can organize themselves on their own using the nucleoid as a scaffold; in turn, they distribute carboxysomes evenly along the length of a cell. Plants also obtain their energy from the sun via photosynthesis, but they do not carry carboxysomes. Scientists have tried to introduce these compartments inside plant cells, hoping that it could generate crops with higher yields. Knowing how carboxysomes are organized so they can be passed down from one generation to the next could be important for these experiments.
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Affiliation(s)
- Joshua S MacCready
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Pusparanee Hakim
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Michigan, United States
| | - Eric J Young
- Department of Biochemistry, Michigan State University, East Lansing, United States
| | - Longhua Hu
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jian Liu
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | | | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Michigan, United States
| | - Daniel C Ducat
- Department of Biochemistry, Michigan State University, East Lansing, United States.,MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
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155
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Noreña-Caro D, Benton MG. Cyanobacteria as photoautotrophic biofactories of high-value chemicals. J CO2 UTIL 2018. [DOI: 10.1016/j.jcou.2018.10.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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156
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South PF, Cavanagh AP, Lopez-Calcagno PE, Raines CA, Ort DR. Optimizing photorespiration for improved crop productivity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1217-1230. [PMID: 30126060 DOI: 10.1111/jipb.12709] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 08/14/2018] [Indexed: 05/24/2023]
Abstract
In C3 plants, photorespiration is an energy-expensive process, including the oxygenation of ribulose-1,5-bisphosphate (RuBP) by ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and the ensuing multi-organellar photorespiratory pathway required to recycle the toxic byproducts and recapture a portion of the fixed carbon. Photorespiration significantly impacts crop productivity through reducing yields in C3 crops by as much as 50% under severe conditions. Thus, reducing the flux through, or improving the efficiency of photorespiration has the potential of large improvements in C3 crop productivity. Here, we review an array of approaches intended to engineer photorespiration in a range of plant systems with the goal of increasing crop productivity. Approaches include optimizing flux through the native photorespiratory pathway, installing non-native alternative photorespiratory pathways, and lowering or even eliminating Rubisco-catalyzed oxygenation of RuBP to reduce substrate entrance into the photorespiratory cycle. Some proposed designs have been successful at the proof of concept level. A plant systems-engineering approach, based on new opportunities available from synthetic biology to implement in silico designs, holds promise for further progress toward delivering more productive crops to farmer's fields.
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Affiliation(s)
- Paul F South
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture/Agricultural Research Service, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Amanda P Cavanagh
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | | | - Christine A Raines
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA
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157
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Dai W, Chen M, Myers C, Ludtke SJ, Pettitt BM, King JA, Schmid MF, Chiu W. Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography. J Mol Biol 2018; 430:4156-4167. [PMID: 30138616 DOI: 10.1016/j.jmb.2018.08.013.visualizing] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/29/2018] [Accepted: 08/13/2018] [Indexed: 05/19/2023]
Abstract
Cyanobacteria are photosynthetic organisms responsible for ~25% of the organic carbon fixation on earth. A key step in carbon fixation is catalyzed by ribulose bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme in the biosphere. Applying Zernike phase-contrast electron cryo-tomography and automated annotation, we identified individual RuBisCO molecules and their assembly intermediates leading to the formation of carboxysomes inside Syn5 cyanophage infected cyanobacteria Synechococcus sp. WH8109 cells. Surprisingly, more RuBisCO molecules were found to be present as cytosolic free-standing complexes or clusters than as packaged assemblies inside carboxysomes. Cytosolic RuBisCO clusters and partially assembled carboxysomes identified in the cell tomograms support a concurrent assembly model involving both the protein shell and the enclosed RuBisCO. In mature carboxysomes, RuBisCO is neither randomly nor strictly icosahedrally packed within protein shells of variable sizes. A time-averaged molecular dynamics simulation showed a semi-liquid probability distribution of the RuBisCO in carboxysomes and correlated well with carboxysome subtomogram averages. Our structural observations reveal the various stages of RuBisCO assemblies, which could be important for understanding cellular function.
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Affiliation(s)
- Wei Dai
- Department of Cell Biology and Neuroscience & Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Muyuan Chen
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Myers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven J Ludtke
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - B Montgomery Pettitt
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jonathan A King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA; Departments of Bioengineering and of Microbiology and Immunoplogy, James H. Clark Center, Stanford University, Stanford, CA 94305, USA.
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158
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Herrero A, Flores E. Genetic responses to carbon and nitrogen availability in Anabaena. Environ Microbiol 2018; 21:1-17. [PMID: 30066380 DOI: 10.1111/1462-2920.14370] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/27/2018] [Accepted: 07/29/2018] [Indexed: 11/27/2022]
Abstract
Heterocyst-forming cyanobacteria are filamentous organisms that perform oxygenic photosynthesis and CO2 fixation in vegetative cells and nitrogen fixation in heterocysts, which are formed under deprivation of combined nitrogen. These organisms can acclimate to use different sources of nitrogen and respond to different levels of CO2 . Following work mainly done with the best studied heterocyst-forming cyanobacterium, Anabaena, here we summarize the mechanisms of assimilation of ammonium, nitrate, urea and N2 , the latter involving heterocyst differentiation, and describe aspects of CO2 assimilation that involves a carbon concentration mechanism. These processes are subjected to regulation establishing a hierarchy in the assimilation of nitrogen sources -with preference for the most reduced nitrogen forms- and a dependence on sufficient carbon. This regulation largely takes place at the level of gene expression and is exerted by a variety of transcription factors, including global and pathway-specific transcriptional regulators. NtcA is a CRP-family protein that adjusts global gene expression in response to the C-to-N balance in the cells, and PacR is a LysR-family transcriptional regulator (LTTR) that extensively acclimates the cells to oxygenic phototrophy. A cyanobacterial-specific transcription factor, HetR, is involved in heterocyst differentiation, and other LTTR factors are specifically involved in nitrate and CO2 assimilation.
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Affiliation(s)
- Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Américo Vespucio 49, E-41092, Seville, Spain
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Américo Vespucio 49, E-41092, Seville, Spain
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159
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Mahinthichaichan P, Morris DM, Wang Y, Jensen GJ, Tajkhorshid E. Selective Permeability of Carboxysome Shell Pores to Anionic Molecules. J Phys Chem B 2018; 122:9110-9118. [PMID: 30193460 PMCID: PMC6311388 DOI: 10.1021/acs.jpcb.8b06822] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Carboxysomes are closed polyhedral cellular microcompartments that increase the efficiency of carbon fixation in autotrophic bacteria. Carboxysome shells consist of small proteins that form hexameric units with semipermeable central pores containing binding sites for anions. This feature is thought to selectively allow access to RuBisCO enzymes inside the carboxysome by HCO3- (the dominant form of CO2 in the aqueous solution at pH 7.4) but not O2, which leads to a nonproductive reaction. To test this hypothesis, here we use molecular dynamics simulations to characterize the energetics and permeability of CO2, O2, and HCO3- through the central pores of two different shell proteins, namely, CsoS1A of α-carboxysome and CcmK4 of β-carboxysome shells. We find that the central pores are in fact selectively permeable to anions such as HCO3-, as predicted by the model.
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Affiliation(s)
- Paween Mahinthichaichan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801-3028 , United States
| | - Dylan M Morris
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Yi Wang
- Department of Physics , The Chinese University of Hong Kong , Shatin , New Territories, Hong Kong SAR , The People's Republic of China
| | - Grant J Jensen
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Howard Hughes Medical Institute , California Insitute of Technology , Pasadena , California 91125 , United States
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801-3028 , United States
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160
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Long BM, Hee WY, Sharwood RE, Rae BD, Kaines S, Lim YL, Nguyen ND, Massey B, Bala S, von Caemmerer S, Badger MR, Price GD. Carboxysome encapsulation of the CO 2-fixing enzyme Rubisco in tobacco chloroplasts. Nat Commun 2018; 9:3570. [PMID: 30177711 PMCID: PMC6120970 DOI: 10.1038/s41467-018-06044-0] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/12/2018] [Indexed: 12/30/2022] Open
Abstract
A long-term strategy to enhance global crop photosynthesis and yield involves the introduction of cyanobacterial CO2-concentrating mechanisms (CCMs) into plant chloroplasts. Cyanobacterial CCMs enable relatively rapid CO2 fixation by elevating intracellular inorganic carbon as bicarbonate, then concentrating it as CO2 around the enzyme Rubisco in specialized protein micro-compartments called carboxysomes. To date, chloroplastic expression of carboxysomes has been elusive, requiring coordinated expression of almost a dozen proteins. Here we successfully produce simplified carboxysomes, isometric with those of the source organism Cyanobium, within tobacco chloroplasts. We replace the endogenous Rubisco large subunit gene with cyanobacterial Form-1A Rubisco large and small subunit genes, along with genes for two key α-carboxysome structural proteins. This minimal gene set produces carboxysomes, which encapsulate the introduced Rubisco and enable autotrophic growth at elevated CO2. This result demonstrates the formation of α-carboxysomes from a reduced gene set, informing the step-wise construction of fully functional α-carboxysomes in chloroplasts.
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Affiliation(s)
- Benedict M Long
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia.
| | - Wei Yih Hee
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Robert E Sharwood
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Benjamin D Rae
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Sarah Kaines
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Yi-Leen Lim
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Nghiem D Nguyen
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Baxter Massey
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Soumi Bala
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Susanne von Caemmerer
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Murray R Badger
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - G Dean Price
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
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161
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Dai W, Chen M, Myers C, Ludtke SJ, Pettitt BM, King JA, Schmid MF, Chiu W. Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography. J Mol Biol 2018; 430:4156-4167. [PMID: 30138616 DOI: 10.1016/j.jmb.2018.08.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/29/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022]
Abstract
Cyanobacteria are photosynthetic organisms responsible for ~25% of the organic carbon fixation on earth. A key step in carbon fixation is catalyzed by ribulose bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme in the biosphere. Applying Zernike phase-contrast electron cryo-tomography and automated annotation, we identified individual RuBisCO molecules and their assembly intermediates leading to the formation of carboxysomes inside Syn5 cyanophage infected cyanobacteria Synechococcus sp. WH8109 cells. Surprisingly, more RuBisCO molecules were found to be present as cytosolic free-standing complexes or clusters than as packaged assemblies inside carboxysomes. Cytosolic RuBisCO clusters and partially assembled carboxysomes identified in the cell tomograms support a concurrent assembly model involving both the protein shell and the enclosed RuBisCO. In mature carboxysomes, RuBisCO is neither randomly nor strictly icosahedrally packed within protein shells of variable sizes. A time-averaged molecular dynamics simulation showed a semi-liquid probability distribution of the RuBisCO in carboxysomes and correlated well with carboxysome subtomogram averages. Our structural observations reveal the various stages of RuBisCO assemblies, which could be important for understanding cellular function.
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Affiliation(s)
- Wei Dai
- Department of Cell Biology and Neuroscience & Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Muyuan Chen
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Myers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven J Ludtke
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - B Montgomery Pettitt
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jonathan A King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA; Departments of Bioengineering and of Microbiology and Immunoplogy, James H. Clark Center, Stanford University, Stanford, CA 94305, USA.
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162
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Mohajerani F, Hagan MF. The role of the encapsulated cargo in microcompartment assembly. PLoS Comput Biol 2018; 14:e1006351. [PMID: 30063715 PMCID: PMC6086489 DOI: 10.1371/journal.pcbi.1006351] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/10/2018] [Accepted: 07/10/2018] [Indexed: 11/19/2022] Open
Abstract
Bacterial microcompartments are large, roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria. Motivated by microcompartment assembly, we use coarse-grained computational and theoretical modeling to study the factors that control the size and morphology of a protein shell assembling around hundreds to thousands of molecules. We perform dynamical simulations of shell assembly in the presence and absence of cargo over a range of interaction strengths, subunit and cargo stoichiometries, and the shell spontaneous curvature. Depending on these parameters, we find that the presence of a cargo can either increase or decrease the size of a shell relative to its intrinsic spontaneous curvature, as seen in recent experiments. These features are controlled by a balance of kinetic and thermodynamic effects, and the shell size is assembly pathway dependent. We discuss implications of these results for synthetic biology efforts to target new enzymes to microcompartment interiors.
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Affiliation(s)
- Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
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163
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P II-like signaling protein SbtB links cAMP sensing with cyanobacterial inorganic carbon response. Proc Natl Acad Sci U S A 2018; 115:E4861-E4869. [PMID: 29735650 DOI: 10.1073/pnas.1803790115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria are phototrophic prokaryotes that evolved oxygenic photosynthesis ∼2.7 billion y ago and are presently responsible for ∼10% of total global photosynthetic production. To cope with the evolutionary pressure of dropping ambient CO2 concentrations, they evolved a CO2-concentrating mechanism (CCM) to augment intracellular inorganic carbon (Ci) levels for efficient CO2 fixation. However, how cyanobacteria sense the fluctuation in Ci is poorly understood. Here we present biochemical, structural, and physiological insights into SbtB, a unique PII-like signaling protein, which provides new insights into Ci sensing. SbtB is highly conserved in cyanobacteria and is coexpressed with CCM genes. The SbtB protein from the cyanobacterium Synechocystis sp. PCC 6803 bound a variety of adenosine nucleotides, including the second messenger cAMP. Cocrystal structures unraveled the individual binding modes of trimeric SbtB with AMP and cAMP. The nucleotide-binding pocket is located between the subunit clefts of SbtB, perfectly matching the structure of canonical PII proteins. This clearly indicates that proteins of the PII superfamily arose from a common ancestor, whose structurally conserved nucleotide-binding pocket has evolved to sense different adenyl nucleotides for various signaling functions. Moreover, we provide physiological and biochemical evidence for the involvement of SbtB in Ci acclimation. Collectively, our results suggest that SbtB acts as a Ci sensor protein via cAMP binding, highlighting an evolutionarily conserved role for cAMP in signaling the cellular carbon status.
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164
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Abstract
Bacterial microcompartments (BMCs) are self-assembling organelles that consist of an enzymatic core that is encapsulated by a selectively permeable protein shell. The potential to form BMCs is widespread and found across the kingdom Bacteria. BMCs have crucial roles in carbon dioxide fixation in autotrophs and the catabolism of organic substrates in heterotrophs. They contribute to the metabolic versatility of bacteria, providing a competitive advantage in specific environmental niches. Although BMCs were first visualized more than 60 years ago, it is mainly in the past decade that progress has been made in understanding their metabolic diversity and the structural basis of their assembly and function. This progress has not only heightened our understanding of their role in microbial metabolism but is also beginning to enable their use in a variety of applications in synthetic biology. In this Review, we focus on recent insights into the structure, assembly, diversity and function of BMCs.
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Affiliation(s)
- Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Clement Aussignargues
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jan Zarzycki
- Max-Planck-Institute for Terrestrial Microbiology, D-35043, Marburg, Germany
| | - Fei Cai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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165
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A Bacterial Microcompartment Is Used for Choline Fermentation by Escherichia coli 536. J Bacteriol 2018; 200:JB.00764-17. [PMID: 29507086 DOI: 10.1128/jb.00764-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/23/2018] [Indexed: 01/16/2023] Open
Abstract
Bacterial choline degradation in the human gut has been associated with cancer and heart disease. In addition, recent studies found that a bacterial microcompartment is involved in choline utilization by Proteus and Desulfovibrio species. However, many aspects of this process have not been fully defined. Here, we investigate choline degradation by the uropathogen Escherichia coli 536. Growth studies indicated E. coli 536 degrades choline primarily by fermentation. Electron microscopy indicated that a bacterial microcompartment was used for this process. Bioinformatic analyses suggested that the choline utilization (cut) gene cluster of E. coli 536 includes two operons, one containing three genes and a main operon of 13 genes. Regulatory studies indicate that the cutX gene encodes a positive transcriptional regulator required for induction of the main cut operon in response to choline supplementation. Each of the 16 genes in the cut cluster was individually deleted, and phenotypes were examined. The cutX, cutY, cutF, cutO, cutC, cutD, cutU, and cutV genes were required for choline degradation, but the remaining genes of the cut cluster were not essential under the conditions used. The reasons for these varied phenotypes are discussed.IMPORTANCE Here, we investigate choline degradation in E. coli 536. These studies provide a basis for understanding a new type of bacterial microcompartment and may provide deeper insight into the link between choline degradation in the human gut and cancer and heart disease. These are also the first studies of choline degradation in E. coli 536, an organism for which sophisticated genetic analysis methods are available. In addition, the cut gene cluster of E. coli 536 is located in pathogenicity island II (PAI-II536) and hence might contribute to pathogenesis.
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166
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Kelly CL, Taylor GM, Hitchcock A, Torres-Méndez A, Heap JT. A Rhamnose-Inducible System for Precise and Temporal Control of Gene Expression in Cyanobacteria. ACS Synth Biol 2018; 7:1056-1066. [PMID: 29544054 DOI: 10.1021/acssynbio.7b00435] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cyanobacteria are important for fundamental studies of photosynthesis and have great biotechnological potential. In order to better study and fully exploit these organisms, the limited repertoire of genetic tools and parts must be expanded. A small number of inducible promoters have been used in cyanobacteria, allowing dynamic external control of gene expression through the addition of specific inducer molecules. However, the inducible promoters used to date suffer from various drawbacks including toxicity of inducers, leaky expression in the absence of inducer and inducer photolability, the latter being particularly relevant to cyanobacteria, which, as photoautotrophs, are grown under light. Here we introduce the rhamnose-inducible rhaBAD promoter of Escherichia coli into the model freshwater cyanobacterium Synechocystis sp. PCC 6803 and demonstrate it has superior properties to previously reported cyanobacterial inducible promoter systems, such as a non-toxic, photostable, non-metabolizable inducer, a linear response to inducer concentration and crucially no basal transcription in the absence of inducer.
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Affiliation(s)
- Ciarán L. Kelly
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - George M. Taylor
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - Andrew Hitchcock
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - Antonio Torres-Méndez
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - John T. Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
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167
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De Porcellinis AJ, Nørgaard H, Brey LMF, Erstad SM, Jones PR, Heazlewood JL, Sakuragi Y. Overexpression of bifunctional fructose-1,6-bisphosphatase/sedoheptulose-1,7-bisphosphatase leads to enhanced photosynthesis and global reprogramming of carbon metabolism in Synechococcus sp. PCC 7002. Metab Eng 2018; 47:170-183. [PMID: 29510212 DOI: 10.1016/j.ymben.2018.03.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/02/2018] [Accepted: 03/01/2018] [Indexed: 12/25/2022]
Abstract
Cyanobacteria fix atmospheric CO2 to biomass and through metabolic engineering can also act as photosynthetic factories for sustainable productions of fuels and chemicals. The Calvin Benson cycle is the primary pathway for CO2 fixation in cyanobacteria, algae and C3 plants. Previous studies have overexpressed the Calvin Benson cycle enzymes, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and bifunctional sedoheptulose-1,7-bisphosphatase/fructose-1,6-bisphosphatase (hereafter BiBPase), in both plants and algae, although their impacts on cyanobacteria have not yet been rigorously studied. Here, we show that overexpression of BiBPase and RuBisCO have distinct impacts on carbon metabolism in the cyanobacterium Synechococcus sp. PCC 7002 through physiological, biochemical, and proteomic analyses. The former enhanced growth, cell size, and photosynthetic O2 evolution, and coordinately upregulated enzymes in the Calvin Benson cycle including RuBisCO and fructose-1,6-bisphosphate aldolase. At the same time it downregulated enzymes in respiratory carbon metabolism (glycolysis and the oxidative pentose phosphate pathway) including glucose-6-phosphate dehydrogenase (G6PDH). The content of glycogen was also significantly reduced while the soluble carbohydrate content increased. These results indicate that overexpression of BiBPase leads to global reprogramming of carbon metabolism in Synechococcus sp. PCC 7002, promoting photosynthetic carbon fixation and carbon partitioning towards non-storage carbohydrates. In contrast, whilst overexpression of RuBisCO had no measurable impact on growth and photosynthetic O2 evolution, it led to coordinated increase in the abundance of proteins involved in pyruvate metabolism and fatty acid biosynthesis. Our results underpin that singular genetic modifications in the Calvin Benson cycle can have far broader cellular impact than previously expected. These features could be exploited to more efficiently direct carbons towards desired bioproducts.
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Affiliation(s)
- Alice Jara De Porcellinis
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark; Carlsberg Research Laboratory, 100 Ny Carlsberg Vej, 1799 Copenhagen V, Denmark
| | - Hanne Nørgaard
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark; Novo Nordisk, Novo Nordisk Park 1, 2760 Måløv, Denmark
| | - Laura Maria Furelos Brey
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark
| | - Simon Matthé Erstad
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark
| | - Patrik R Jones
- Department Life Sciences, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, UK
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Yumiko Sakuragi
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark.
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168
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Fang Y, Huang F, Faulkner M, Jiang Q, Dykes GF, Yang M, Liu LN. Engineering and Modulating Functional Cyanobacterial CO 2-Fixing Organelles. FRONTIERS IN PLANT SCIENCE 2018; 9:739. [PMID: 29922315 PMCID: PMC5996877 DOI: 10.3389/fpls.2018.00739] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/15/2018] [Indexed: 05/12/2023]
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles widespread among bacterial phyla and provide a means for compartmentalizing specific metabolic pathways. They sequester catalytic enzymes from the cytoplasm, using an icosahedral proteinaceous shell with selective permeability to metabolic molecules and substrates, to enhance metabolic efficiency. Carboxysomes were the first BMCs discovered and their unprecedented capacity of CO2 fixation allows cyanobacteria to make a significant contribution to global carbon fixation. There is an increasing interest in utilizing synthetic biology to construct synthetic carboxysomes in new hosts, i.e., higher plants, to enhance carbon fixation and productivity. Here, we report the construction of a synthetic operon of the β-carboxysome from the cyanobacterium Synechococcus elongatus PCC7942 to generate functional β-carboxysome-like structures in Escherichia coli. The protein expression, structure, assembly, and activity of synthetic β-carboxysomes were characterized in depth using confocal, electron and atomic force microscopy, proteomics, immunoblot analysis, and enzymatic assays. Furthermore, we examined the in vivo interchangeability of β-carboxysome building blocks with other BMC components. To our knowledge, this is the first production of functional β-carboxysome-like structures in heterologous organisms. It provides important information for the engineering of fully functional carboxysomes and CO2-fixing modules in higher plants. The study strengthens our synthetic biology toolbox for generating BMC-based organelles with tunable activities and new scaffolding biomaterials for metabolic improvement and molecule delivery.
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169
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Azuma Y, Edwardson TGW, Hilvert D. Tailoring lumazine synthase assemblies for bionanotechnology. Chem Soc Rev 2018; 47:3543-3557. [DOI: 10.1039/c8cs00154e] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The cage-forming protein lumazine synthase is readily modified, evolved and assembled with other components.
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Affiliation(s)
- Yusuke Azuma
- Laboratory of Organic Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
| | | | - Donald Hilvert
- Laboratory of Organic Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
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170
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The Wrappers of the 1,2-Propanediol Utilization Bacterial Microcompartments. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1112:333-344. [DOI: 10.1007/978-981-13-3065-0_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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171
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Rodriguez-Ramos J, Faulkner M, Liu LN. Nanoscale Visualization of Bacterial Microcompartments Using Atomic Force Microscopy. Methods Mol Biol 2018; 1814:373-383. [PMID: 29956244 DOI: 10.1007/978-1-4939-8591-3_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial microcompartments (BMCs) are polyhedral protein organelles in many prokaryotes, playing significant roles in metabolic enhancement. Due to their self-assembly and modularity nature, BMCs have gained increased interest in recent years, with the intent of constructing new nanobioreactors and scaffolding to promote cellular metabolisms and molecule delivery. In this chapter, we describe the technique of atomic force microscopy (AFM) as a method to study the self-assembly dynamics and physical properties of BMCs. We focus on the sample preparation, the measurement procedure, and the data analysis for high-speed AFM imaging and nanoindentation-based spectroscopy, which were used to determine the assembly dynamics of BMC shell proteins and the nanomechanics of intact BMC structures, respectively. The described methods could be applied to the study of other types of self-assembling biological organelles.
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Affiliation(s)
| | - Matthew Faulkner
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
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172
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Tomar V, Sidhu GK, Nogia P, Mehrotra R, Mehrotra S. Regulatory components of carbon concentrating mechanisms in aquatic unicellular photosynthetic organisms. PLANT CELL REPORTS 2017; 36:1671-1688. [PMID: 28780704 DOI: 10.1007/s00299-017-2191-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 07/31/2017] [Indexed: 06/07/2023]
Abstract
This review provides an insight into the regulation of the carbon concentrating mechanisms (CCMs) in lower organisms like cyanobacteria, proteobacteria, and algae. CCMs evolved as a mechanism to concentrate CO2 at the site of primary carboxylating enzyme Ribulose-1, 5-bisphosphate carboxylase oxygenase (Rubisco), so that the enzyme could overcome its affinity towards O2 which leads to wasteful processes like photorespiration. A diverse set of CCMs exist in nature, i.e., carboxysomes in cyanobacteria and proteobacteria; pyrenoids in algae and diatoms, the C4 system, and Crassulacean acid metabolism in higher plants. Prime regulators of CCM in most of the photosynthetic autotrophs belong to the LysR family of transcriptional regulators, which regulate the activity of the components of CCM depending upon the ambient CO2 concentrations. Major targets of these regulators are carbonic anhydrase and inorganic carbon uptake systems (CO2 and HCO3- transporters) whose activities are modulated either at transcriptional level or by changes in the levels of their co-regulatory metabolites. The article provides information on the localization of the CCM components as well as their function and participation in the development of an efficient CCM. Signal transduction cascades leading to activation/inactivation of inducible CCM components on perception of low/high CO2 stimuli have also been brought into picture. A detailed study of the regulatory components can aid in identifying the unraveled aspects of these mechanisms and hence provide information on key molecules that need to be explored to further provide a clear understanding of the mechanism under study.
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Affiliation(s)
- Vandana Tomar
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, 333031, Rajasthan, India
| | - Gurpreet Kaur Sidhu
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, 333031, Rajasthan, India
| | - Panchsheela Nogia
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, 333031, Rajasthan, India
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, 333031, Rajasthan, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, 333031, Rajasthan, India.
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173
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Niederhuber MJ, Lambert TJ, Yapp C, Silver PA, Polka JK. Superresolution microscopy of the β-carboxysome reveals a homogeneous matrix. Mol Biol Cell 2017; 28:2734-2745. [PMID: 28963440 PMCID: PMC5620380 DOI: 10.1091/mbc.e17-01-0069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 07/26/2017] [Accepted: 08/02/2017] [Indexed: 11/11/2022] Open
Abstract
Carbon fixation in cyanobacteria makes a major contribution to the global carbon cycle. The cyanobacterial carboxysome is a proteinaceous microcompartment that protects and concentrates the carbon-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) in a paracrystalline lattice, making it possible for these organisms to fix CO2 from the atmosphere. The protein responsible for the organization of this lattice in beta-type carboxysomes of the freshwater cyanobacterium Synechococcus elongatus, CcmM, occurs in two isoforms thought to localize differentially within the carboxysome matrix. Here we use wide-field time-lapse and three-dimensional structured illumination microscopy (3D-SIM) to study the recruitment and localization of these two isoforms. We demonstrate that this superresolution technique is capable of distinguishing the localizations of the outer protein shell of the carboxysome and its internal cargo. We develop an automated analysis pipeline to analyze and quantify 3D-SIM images and generate a population-level description of the carboxysome shell protein, RuBisCO, and CcmM isoform localization. We find that both CcmM isoforms have similar spatial and temporal localization, prompting a revised model of the internal arrangement of the β-carboxysome.
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Affiliation(s)
- Matthew J Niederhuber
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Talley J Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Clarence Yapp
- Image and Data Analysis Core, Harvard Medical School, Boston, MA 02115
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Jessica K Polka
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
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174
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Ogbaga CC, Stepien P, Athar HUR, Ashraf M. Engineering Rubisco activase from thermophilic cyanobacteria into high-temperature sensitive plants. Crit Rev Biotechnol 2017; 38:559-572. [DOI: 10.1080/07388551.2017.1378998] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Chukwuma C. Ogbaga
- Department of Biological Sciences, Nile University of Nigeria, Abuja, Nigeria
| | - Piotr Stepien
- Department of Plant Nutrition, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Habib-Ur-Rehman Athar
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
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175
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Baumgart M, Huber I, Abdollahzadeh I, Gensch T, Frunzke J. Heterologous expression of the Halothiobacillus neapolitanus carboxysomal gene cluster in Corynebacterium glutamicum. J Biotechnol 2017; 258:126-135. [DOI: 10.1016/j.jbiotec.2017.03.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/16/2017] [Accepted: 03/18/2017] [Indexed: 12/20/2022]
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176
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Turmo A, Gonzalez-Esquer CR, Kerfeld CA. Carboxysomes: metabolic modules for CO2 fixation. FEMS Microbiol Lett 2017; 364:4082729. [DOI: 10.1093/femsle/fnx176] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/12/2017] [Indexed: 11/13/2022] Open
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177
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Faulkner M, Rodriguez-Ramos J, Dykes GF, Owen SV, Casella S, Simpson DM, Beynon RJ, Liu LN. Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes. NANOSCALE 2017; 9:10662-10673. [PMID: 28616951 PMCID: PMC5708340 DOI: 10.1039/c7nr02524f] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Carboxysomes are proteinaceous organelles that play essential roles in enhancing carbon fixation in cyanobacteria and some proteobacteria. These self-assembling organelles encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase using a protein shell structurally resembling an icosahedral viral capsid. The protein shell serves as a physical barrier to protect enzymes from the cytosol and a selectively permeable membrane to mediate transport of enzyme substrates and products. The structural and mechanical nature of native carboxysomes remain unclear. Here, we isolate functional β-carboxysomes from the cyanobacterium Synechococcus elongatus PCC7942 and perform the first characterization of the macromolecular architecture and inherent physical mechanics of single β-carboxysomes using electron microscopy, atomic force microscopy (AFM) and proteomics. Our results illustrate that the intact β-carboxysome comprises three structural domains, a single-layered icosahedral shell, an inner layer and paracrystalline arrays of interior Rubisco. We also observe the protein organization of the shell and partial β-carboxysomes that likely serve as the β-carboxysome assembly intermediates. Furthermore, the topography and intrinsic mechanics of functional β-carboxysomes are determined in native conditions using AFM and AFM-based nanoindentation, revealing the flexible organization and soft mechanical properties of β-carboxysomes compared to rigid viruses. Our study provides new insights into the natural characteristics of β-carboxysome organization and nanomechanics, which can be extended to diverse bacterial microcompartments and are important considerations for the design and engineering of functional carboxysomes in other organisms to supercharge photosynthesis. It offers an approach for inspecting the structural and mechanical features of synthetic metabolic organelles and protein scaffolds in bioengineering.
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Affiliation(s)
- Matthew Faulkner
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | | | - Gregory F Dykes
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Siân V Owen
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Selene Casella
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Deborah M Simpson
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Robert J Beynon
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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178
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Larsson AM, Hasse D, Valegård K, Andersson I. Crystal structures of β-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3857-3867. [PMID: 28369612 PMCID: PMC5853799 DOI: 10.1093/jxb/erx070] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/15/2017] [Indexed: 05/21/2023]
Abstract
Cyanobacterial CO2 fixation is promoted by encapsulating and co-localizing the CO2-fixing enzymes within a protein shell, the carboxysome. A key feature of the carboxysome is its ability to control selectively the flux of metabolites in and out of the shell. The β-carboxysome shell protein CcmP has been shown to form a double layer of pseudohexamers with a relatively large central pore (~13 Å diameter), which may allow passage of larger metabolites such as the substrate for CO2 fixation, ribulose 1,5-bisphosphate, through the shell. Here we describe two crystal structures, at 1.45 Å and 1.65 Å resolution, of CcmP from Synechococcus elongatus PCC7942 (SeCcmP). The central pore of CcmP is open or closed at its ends, depending on the conformation of two conserved residues, Glu69 and Arg70. The presence of glycerol resulted in a pore that is open at one end and closed at the opposite end. When glycerol was omitted, both ends of the barrel became closed. A binding pocket at the interior of the barrel featured residual density with distinct differences in size and shape depending on the conformation, open or closed, of the central pore of SeCcmP, suggestive of a metabolite-driven mechanism for the gating of the pore.
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Affiliation(s)
- Anna M Larsson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan, Uppsala, Sweden
- Correspondence:
| | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan, Uppsala, Sweden
| | - Karin Valegård
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan, Uppsala, Sweden
| | - Inger Andersson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan, Uppsala, Sweden
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179
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Kaplan A. On the cradle of CCM research: discovery, development, and challenges ahead. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3785-3796. [PMID: 28520892 DOI: 10.1093/jxb/erx122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Herein, 40 years after its discovery, I briefly and critically survey the development of ideas that propelled research on CO2-concentrating mechanisms (CCMs; a term proposed by Dean Price) of phytoplankton, mainly focusing on cyanobacteria. This is not a comprehensive review on CCM research, but a personal view on the past developments and challenges that lie ahead.
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Affiliation(s)
- Aaron Kaplan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Israel
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180
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Young JN, Hopkinson BM. The potential for co-evolution of CO2-concentrating mechanisms and Rubisco in diatoms. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3751-3762. [PMID: 28645158 DOI: 10.1093/jxb/erx130] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Diatoms are a diverse group of unicellular algae that contribute significantly to global photosynthetic carbon fixation and export in the modern ocean, and are an important source of microfossils for paleoclimate reconstructions. Because of their importance in the environment, diatoms have been a focus of study on the physiology and ecophysiology of carbon fixation, in particular their CO2-concentrating mechanisms (CCMs) and Rubisco characteristics. While carbon fixation in diatoms is not as well understood as in certain model aquatic photoautotrophs, a greater number of species have been examined in diatoms. Recent work has highlighted a large diversity in the function, physiology, and kinetics of both the CCM and Rubisco between different diatom species. This diversity was unexpected since it has generally been assumed that CCMs and Rubiscos were similar within major algal lineages as the result of selective events deep in evolutionary history, and suggests a more recent co-evolution between the CCM and Rubisco within diatoms. This review explores our current understanding of the diatom CCM and highlights the diversity of both the CCM and Rubisco kinetics. We will suggest possible environmental, physiological, and evolutionary drivers for the co-evolution of the CCM and Rubisco in diatoms.
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Affiliation(s)
- Jodi N Young
- University of Washington, School of Oceanography, Seattle, WA 98105, USA
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181
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Sommer M, Cai F, Melnicki M, Kerfeld CA. β-Carboxysome bioinformatics: identification and evolution of new bacterial microcompartment protein gene classes and core locus constraints. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3841-3855. [PMID: 28419380 PMCID: PMC5853843 DOI: 10.1093/jxb/erx115] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/18/2017] [Indexed: 05/03/2023]
Abstract
Carboxysomes are bacterial microcompartments (BMCs) that enhance CO2 fixation in all cyanobacteria. Structurally, carboxysome shell proteins are classified according to the type of oligomer formed: hexameric (BMC-H), trimeric (BMC-T) and pentameric (BMC-P) proteins. To understand the forces driving the evolution of the carboxysome shell, we conducted a bioinformatic study of genes encoding β-carboxysome shell proteins, taking advantage of the recent large increase in sequenced cyanobacterial genomes. In addition to the four well-established BMC-H (CcmK1-4) classes, our analysis reveals two new CcmK classes, which we name CcmK5 and CcmK6. CcmK5 is phylogenetically closest to CcmK3 and CcmK4, and the ccmK5 gene is found only in genomes lacking ccmK3 and ccmk4 genes. ccmK6 is found predominantly in heterocyst-forming cyanobacteria. The gene encoding the BMC-T homolog CcmO is associated with the main carboxysome locus (MCL) in only 60% of all species. We find five evolutionary origins of separation of ccmO from the MCL. Transcriptome analysis demonstrates that satellite ccmO genes, in contrast to MCL-associated ccmO genes, are never co-regulated with other MCL genes. The dispersal of carboxysome shell genes across the genome allows for distinct regulation of their expression, perhaps in response to changes in environmental conditions.
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Affiliation(s)
- Manuel Sommer
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fei Cai
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew Melnicki
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cheryl A Kerfeld
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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182
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Rae BD, Long BM, Förster B, Nguyen ND, Velanis CN, Atkinson N, Hee WY, Mukherjee B, Price GD, McCormick AJ. Progress and challenges of engineering a biophysical CO2-concentrating mechanism into higher plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3717-3737. [PMID: 28444330 DOI: 10.1093/jxb/erx133] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Growth and productivity in important crop plants is limited by the inefficiencies of the C3 photosynthetic pathway. Introducing CO2-concentrating mechanisms (CCMs) into C3 plants could overcome these limitations and lead to increased yields. Many unicellular microautotrophs, such as cyanobacteria and green algae, possess highly efficient biophysical CCMs that increase CO2 concentrations around the primary carboxylase enzyme, Rubisco, to enhance CO2 assimilation rates. Algal and cyanobacterial CCMs utilize distinct molecular components, but share several functional commonalities. Here we outline the recent progress and current challenges of engineering biophysical CCMs into C3 plants. We review the predicted requirements for a functional biophysical CCM based on current knowledge of cyanobacterial and algal CCMs, the molecular engineering tools and research pipelines required to translate our theoretical knowledge into practice, and the current challenges to achieving these goals.
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Affiliation(s)
- Benjamin D Rae
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Benedict M Long
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Britta Förster
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Nghiem D Nguyen
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Christos N Velanis
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nicky Atkinson
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Wei Yih Hee
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Bratati Mukherjee
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - G Dean Price
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Alistair J McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
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183
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Mueller-Cajar O. The Diverse AAA+ Machines that Repair Inhibited Rubisco Active Sites. Front Mol Biosci 2017; 4:31. [PMID: 28580359 PMCID: PMC5437159 DOI: 10.3389/fmolb.2017.00031] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/29/2017] [Indexed: 11/13/2022] Open
Abstract
Gaseous carbon dioxide enters the biosphere almost exclusively via the active site of the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). This highly conserved catalyst has an almost universal propensity to non-productively interact with its substrate ribulose 1,5-bisphosphate, leading to the formation of dead-end inhibited complexes. In diverse autotrophic organisms this tendency has been counteracted by the recruitment of dedicated AAA+ (ATPases associated with various cellular activities) proteins that all use the energy of ATP hydrolysis to remodel inhibited Rubisco active sites leading to release of the inhibitor. Three evolutionarily distinct classes of these Rubisco activases (Rcas) have been discovered so far. Green and red-type Rca are mostly found in photosynthetic eukaryotes of the green and red plastid lineage respectively, whereas CbbQO is associated with chemoautotrophic bacteria. Ongoing mechanistic studies are elucidating how the various motors are utilizing both similar and contrasting strategies to ultimately perform their common function of cracking the inhibited Rubisco active site. The best studied mechanism utilized by red-type Rca appears to involve transient threading of the Rubisco large subunit C-terminal peptide, reminiscent of the action performed by Clp proteases. As well as providing a fascinating example of convergent molecular evolution, Rca proteins can be considered promising crop-improvement targets. Approaches aiming to replace Rubisco in plants with improved enzymes will need to ensure the presence of a compatible Rca protein. The thermolability of the Rca protein found in crop plants provides an opportunity to fortify photosynthesis against high temperature stress. Photosynthesis also appears to be limited by Rca when light conditions are fluctuating. Synthetic biology strategies aiming to enhance the autotrophic CO2 fixation machinery will need to take into consideration the requirement for Rubisco activases as well as their properties.
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Affiliation(s)
- Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological UniversitySingapore, Singapore
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184
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Huttanus HM, Feng X. Compartmentalized metabolic engineering for biochemical and biofuel production. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700052] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/07/2017] [Accepted: 03/20/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Herbert M. Huttanus
- Biological Systems Engineering; Virginia Polytechnic Institute and State University; Blacksburg VA USA
| | - Xueyang Feng
- Biological Systems Engineering; Virginia Polytechnic Institute and State University; Blacksburg VA USA
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185
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The N Terminus of the PduB Protein Binds the Protein Shell of the Pdu Microcompartment to Its Enzymatic Core. J Bacteriol 2017; 199:JB.00785-16. [PMID: 28138097 DOI: 10.1128/jb.00785-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/20/2017] [Indexed: 12/12/2022] Open
Abstract
Bacterial microcompartments (MCPs) are extremely large proteinaceous organelles that consist of an enzymatic core encapsulated within a complex protein shell. A key question in MCP biology is the nature of the interactions that guide the assembly of thousands of protein subunits into a well-ordered metabolic compartment. In this report, we show that the N-terminal 37 amino acids of the PduB protein have a critical role in binding the shell of the 1,2-propanediol utilization (Pdu) microcompartment to its enzymatic core. Several mutations were constructed that deleted short regions of the N terminus of PduB. Growth tests indicated that three of these deletions were impaired MCP assembly. Attempts to purify MCPs from these mutants, followed by gel electrophoresis and enzyme assays, indicated that the protein complexes isolated consisted of MCP shells depleted of core enzymes. Electron microscopy substantiated these findings by identifying apparently empty MCP shells but not intact MCPs. Analyses of 13 site-directed mutants indicated that the key region of the N terminus of PduB required for MCP assembly is a putative helix spanning residues 6 to 18. Considering the findings presented here together with prior work, we propose a new model for MCP assembly.IMPORTANCE Bacterial microcompartments consist of metabolic enzymes encapsulated within a protein shell and are widely used to optimize metabolic process. Here, we show that the N-terminal 37 amino acids of the PduB shell protein are essential for assembly of the 1,2-propanediol utilization microcompartment. The results indicate that it plays a key role in binding the outer shell to the enzymatic core. We propose that this interaction might be used to define the relative orientation of the shell with respect to the core. This finding is of fundamental importance to our understanding of microcompartment assembly and may have application to engineering microcompartments as nanobioreactors for chemical production.
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186
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Hinzpeter F, Gerland U, Tostevin F. Optimal Compartmentalization Strategies for Metabolic Microcompartments. Biophys J 2017; 112:767-779. [PMID: 28256236 PMCID: PMC5340097 DOI: 10.1016/j.bpj.2016.11.3194] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 11/18/2016] [Accepted: 11/28/2016] [Indexed: 11/16/2022] Open
Abstract
Intracellular compartmentalization of cooperating enzymes is a strategy that is frequently used by cells. Segregation of enzymes that catalyze sequential reactions can alleviate challenges such as toxic pathway intermediates, competing metabolic reactions, and slow reaction rates. Inspired by nature, synthetic biologists also seek to encapsulate engineered metabolic pathways within vesicles or proteinaceous shells to enhance the yield of industrially and pharmaceutically useful products. Although enzymatic compartments have been extensively studied experimentally, a quantitative understanding of the underlying design principles is still lacking. Here, we study theoretically how the size and enzymatic composition of compartments should be chosen so as to maximize the productivity of a model metabolic pathway. We find that maximizing productivity requires compartments larger than a certain critical size. The enzyme density within each compartment should be tuned according to a power-law scaling in the compartment size. We explain these observations using an analytically solvable, well-mixed approximation. We also investigate the qualitatively different compartmentalization strategies that emerge in parameter regimes where this approximation breaks down. Our results suggest that the different sizes and enzyme packings of α- and β-carboxysomes each constitute an optimal compartmentalization strategy given the properties of their respective protein shells.
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Affiliation(s)
- Florian Hinzpeter
- Department of Physics, Technische Universität München, Garching, Germany.
| | - Ulrich Gerland
- Department of Physics, Technische Universität München, Garching, Germany
| | - Filipe Tostevin
- Department of Physics, Technische Universität München, Garching, Germany
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187
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Berben T, Overmars L, Sorokin DY, Muyzer G. Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes. Front Microbiol 2017; 8:254. [PMID: 28293216 PMCID: PMC5328954 DOI: 10.3389/fmicb.2017.00254] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/07/2017] [Indexed: 12/21/2022] Open
Abstract
Thiocyanate is a C1 compound containing carbon, nitrogen, and sulfur. It is a (by)product in a number of natural and industrial processes. Because thiocyanate is toxic to many organisms, including humans, its removal from industrial waste streams is an important problem. Although a number of bacteria can use thiocyanate as a nitrogen source, only a few can use it as an electron donor. There are two distinct pathways to use thiocyanate: (i) the “carbonyl sulfide pathway,” which has been extensively studied, and (ii) the “cyanate pathway,” whose key enzyme, thiocyanate dehydrogenase, was recently purified and studied. Three species of Thioalkalivibrio, a group of haloalkaliphilic sulfur-oxidizing bacteria isolated from soda lakes, have been described as thiocyanate oxidizers: (i) Thioalkalivibrio paradoxus (“cyanate pathway”), (ii) Thioalkalivibrio thiocyanoxidans (“cyanate pathway”) and (iii) Thioalkalivibrio thiocyanodenitrificans (“carbonyl sulfide pathway”). In this study we provide a comparative genome analysis of these described thiocyanate oxidizers, with genomes ranging in size from 2.5 to 3.8 million base pairs. While focusing on thiocyanate degradation, we also analyzed the differences in sulfur, carbon, and nitrogen metabolism. We found that the thiocyanate dehydrogenase gene is present in 10 different Thioalkalivibrio strains, in two distinct genomic contexts/genotypes. The first genotype is defined by having genes for flavocytochrome c sulfide dehydrogenase upstream from the thiocyanate dehydrogenase operon (present in two strains including the type strain of Tv. paradoxus), whereas in the second genotype these genes are located downstream, together with two additional genes of unknown function (present in eight strains, including the type strains of Tv. thiocyanoxidans). Additionally, we found differences in the presence/absence of genes for various sulfur oxidation pathways, such as sulfide:quinone oxidoreductase, dissimilatory sulfite reductase, and sulfite dehydrogenase. One strain (Tv. thiocyanodenitrificans) lacks genes encoding a carbon concentrating mechanism and none of the investigated genomes were shown to contain known bicarbonate transporters. This study gives insight into the genomic variation of thiocyanate oxidizing bacteria and may lead to improvements in the application of these organisms in the bioremediation of industrial waste streams.
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Affiliation(s)
- Tom Berben
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, Netherlands
| | - Lex Overmars
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, Netherlands
| | - Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of SciencesMoscow, Russia; Department of Biotechnology, Delft University of TechnologyDelft, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, Netherlands
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188
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Responses of the marine diatom Thalassiosira pseudonana to changes in CO 2 concentration: a proteomic approach. Sci Rep 2017; 7:42333. [PMID: 28181560 PMCID: PMC5299434 DOI: 10.1038/srep42333] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 01/10/2017] [Indexed: 12/18/2022] Open
Abstract
The concentration of CO2 in many aquatic systems is variable, often lower than the KM of the primary carboxylating enzyme Rubisco, and in order to photosynthesize efficiently, many algae operate a facultative CO2 concentrating mechanism (CCM). Here we measured the responses of a marine diatom, Thalassiosira pseudonana, to high and low concentrations of CO2 at the level of transcripts, proteins and enzyme activity. Low CO2 caused many metabolic pathways to be remodeled. Carbon acquisition enzymes, primarily carbonic anhydrase, stress, degradation and signaling proteins were more abundant while proteins associated with nitrogen metabolism, energy production and chaperones were less abundant. A protein with similarities to the Ca2+/ calmodulin dependent protein kinase II_association domain, having a chloroplast targeting sequence, was only present at low CO2. This protein might be a specific response to CO2 limitation since a previous study showed that other stresses caused its reduction. The protein sequence was found in other marine diatoms and may play an important role in their response to low CO2 concentration.
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189
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Leão P, Chen YR, Abreu F, Wang M, Zhang WJ, Zhou K, Xiao T, Wu LF, Lins U. Ultrastructure of ellipsoidal magnetotactic multicellular prokaryotes depicts their complex assemblage and cellular polarity in the context of magnetotaxis. Environ Microbiol 2017; 19:2151-2163. [PMID: 28120460 DOI: 10.1111/1462-2920.13677] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/11/2017] [Accepted: 01/18/2017] [Indexed: 11/28/2022]
Abstract
Magnetotactic multicellular prokaryotes (MMPs) consist of unique microorganisms formed by genetically identical Gram-negative bacterial that live as a single individual capable of producing magnetic nano-particles called magnetosomes. Two distinct morphotypes of MMPs are known: spherical MMPs (sMMPs) and ellipsoidal MMPs (eMMPs). sMMPs have been extensively characterized, but less information exists for eMMPs. Here, we report the ultrastructure and organization as well as gene clusters responsible for magnetosome and flagella biosynthesis in the magnetite magnetosome producer eMMP Candidatus Magnetananas rongchenensis. Transmission electron microscopy and focused ion beam scanning electron microscopy (FIB-SEM) 3D reconstruction reveal that cells with a conspicuous core-periphery polarity were organized around a central space. Magnetosomes were organized in multiple chains aligned along the periphery of each cell. In the partially sequenced genome, magnetite-related mamAB gene and mad gene clusters were identified. Two cell morphologies were detected: irregular elliptical conical 'frustum-like' (IECF) cells and H-shaped cells. IECF cells merge to form H-shaped cells indicating a more complex structure and possibly a distinct evolutionary position of eMMPs when compared with sMMPs considering multicellularity.
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Affiliation(s)
- Pedro Leão
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Yi-Ran Chen
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,CNRS, Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL), Marseille, France
| | - Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Mingling Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Wei-Jia Zhang
- CNRS, Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL), Marseille, France.,Laboratory of Deep Sea Microbial Cell Biology, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Ke Zhou
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Tian Xiao
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,CNRS, Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL), Marseille, France
| | - Long-Fei Wu
- CNRS, Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL), Marseille, France.,Aix Marseille Univ, CNRS, LCB, Marseille, France
| | - Ulysses Lins
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
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190
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Allosteric Inhibition of Phosphoenolpyruvate Carboxylases is Determined by a Single Amino Acid Residue in Cyanobacteria. Sci Rep 2017; 7:41080. [PMID: 28117365 PMCID: PMC5259782 DOI: 10.1038/srep41080] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/14/2016] [Indexed: 01/04/2023] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is an important enzyme for CO2 fixation and primary metabolism in photosynthetic organisms including cyanobacteria. The kinetics and allosteric regulation of PEPCs have been studied in many organisms, but the biochemical properties of PEPC in the unicellular, non-nitrogen-fixing cyanobacterium Synechocystis sp. PCC 6803 have not been clarified. In this study, biochemical analysis revealed that the optimum pH and temperature of Synechocystis 6803 PEPC proteins were 7.3 and 30 °C, respectively. Synechocystis 6803 PEPC was found to be tolerant to allosteric inhibition by several metabolic effectors such as malate, aspartate, and fumarate compared with other cyanobacterial PEPCs. Comparative sequence and biochemical analysis showed that substitution of the glutamate residue at position 954 with lysine altered the enzyme so that it was inhibited by malate, aspartate, and fumarate. PEPC of the nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120 was purified, and its activity was inhibited in the presence of malate. Substitution of the lysine at position 946 (equivalent to position 954 in Synechocystis 6803) with glutamate made Anabaena 7120 PEPC tolerant to malate. These results demonstrate that the allosteric regulation of PEPC in cyanobacteria is determined by a single amino acid residue, a characteristic that is conserved in different orders.
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191
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Rasmussen RE, Erstad SM, Ramos-Martinez EM, Fimognari L, De Porcellinis AJ, Sakuragi Y. An easy and efficient permeabilization protocol for in vivo enzyme activity assays in cyanobacteria. Microb Cell Fact 2016; 15:186. [PMID: 27825349 PMCID: PMC5101802 DOI: 10.1186/s12934-016-0587-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyanobacteria are photosynthetic bacteria that thrive in diverse ecosystems and play major roles in the global carbon cycle. The abilities of cyanobacteria to fix atmospheric CO2 and to allocate the fixed carbons to chemicals and biofuels have attracted growing attentions as sustainable microbial cell factories. Better understanding of the activities of enzymes involved in the central carbon metabolism would lead to increasing product yields. Currently cell-free lysates are the most widely used method for determination of intracellular enzyme activities. However, due to thick cell walls, lysis of cyanobacterial cells is inefficient and often laborious. In some cases radioisotope-labeled substrates can be fed directly to intact cells; however, label-free assays are often favored due to safety and practical reasons. RESULTS Here we show an easy and highly efficient method for permeabilization of the cyanobacteria Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803, and determination of two intracellular enzymes, ribulose-1,5-bisphosphate carboxylase/decarboxylase (Rubisco) and glucose-6-phosphate dehydrogenase (G6PDH), that play pivotal roles in the central carbon metabolism in cyanobacteria. Incubation of the cyanobacterial cells in the commercially available B-PER reagent for 10 min permeabilized the cells, as confirmed by the SYTOX Green staining. There was no significant change in the cell shape and no major loss of intracellular proteins was observed during the treatment. When used directly in the assays, the permeabilized cells exhibited the enzyme activities that are comparable or even higher than those detected for cell-free lysates. Moreover, the permeabilized cells could be stored at -20 °C without losing the enzyme activities. The permeabilization process and subsequent activity assays were successfully adapted to the 96-well plate system. CONCLUSIONS An easy, efficient and scalable permeabilization protocol was established for cyanobacteria. The permeabilized cells can be directly applied for measurement of G6PDH and Rubisco activities without using radioisotopes and the protocol may be readily adapted to studies of other cyanobacterial species and other intracellular enzymes. The permeabilization and enzyme assays can be performed in 96-well plates in a high-throughput manner.
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Affiliation(s)
- Randi Engelberth Rasmussen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark
| | - Simon Matthé Erstad
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark
| | - Erick Miguel Ramos-Martinez
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark
| | - Lorenzo Fimognari
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark
| | - Alice Jara De Porcellinis
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark
| | - Yumiko Sakuragi
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark.
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192
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Wheatley NM, Eden KD, Ngo J, Rosinski JS, Sawaya MR, Cascio D, Collazo M, Hoveida H, Hubbell WL, Yeates TO. A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein. J Mol Biol 2016; 428:4013-4030. [PMID: 27464895 PMCID: PMC5048545 DOI: 10.1016/j.jmb.2016.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/11/2016] [Accepted: 07/18/2016] [Indexed: 11/18/2022]
Abstract
Autotrophic bacteria rely on various mechanisms to increase intracellular concentrations of inorganic forms of carbon (i.e., bicarbonate and CO2) in order to improve the efficiency with which they can be converted to organic forms. Transmembrane bicarbonate transporters and carboxysomes play key roles in accumulating bicarbonate and CO2, but other regulatory elements of carbon concentration mechanisms in bacteria are less understood. In this study, after analyzing the genomic regions around α-type carboxysome operons, we characterize a protein that is conserved across these operons but has not been previously studied. On the basis of a series of apo- and ligand-bound crystal structures and supporting biochemical data, we show that this protein, which we refer to as the carboxysome-associated PII protein (CPII), represents a new and distinct subfamily within the broad superfamily of previously studied PII regulatory proteins, which are generally involved in regulating nitrogen metabolism in bacteria. CPII undergoes dramatic conformational changes in response to ADP binding, and the affinity for nucleotide binding is strongly enhanced by the presence of bicarbonate. CPII therefore appears to be a unique type of PII protein that senses bicarbonate availability, consistent with its apparent genomic association with the carboxysome and its constituents.
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Affiliation(s)
- Nicole M Wheatley
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Kevin D Eden
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Joanna Ngo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Justin S Rosinski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Michael Collazo
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Hamidreza Hoveida
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Wayne L Hubbell
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; Jules Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Todd O Yeates
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
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193
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Comparative Subcellular Localization Analysis of Magnetosome Proteins Reveals a Unique Localization Behavior of Mms6 Protein onto Magnetite Crystals. J Bacteriol 2016; 198:2794-802. [PMID: 27481925 DOI: 10.1128/jb.00280-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/16/2016] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED The magnetosome is an organelle specialized for inorganic magnetite crystal synthesis in magnetotactic bacteria. The complex mechanism of magnetosome formation is regulated by magnetosome proteins in a stepwise manner. Protein localization is a key step for magnetosome development; however, a global study of magnetosome protein localization remains to be conducted. Here, we comparatively analyzed the subcellular localization of a series of green fluorescent protein (GFP)-tagged magnetosome proteins. The protein localizations were categorized into 5 groups (short-length linear, middle-length linear, long-length linear, cell membrane, and intracellular dispersing), which were related to the protein functions. Mms6, which regulates magnetite crystal growth, localized along magnetosome chain structures under magnetite-forming (microaerobic) conditions but was dispersed in the cell under nonforming (aerobic) conditions. Correlative fluorescence and electron microscopy analyses revealed that Mms6 preferentially localized to magnetosomes enclosing magnetite crystals. We suggest that a highly organized spatial regulation mechanism controls magnetosome protein localization during magnetosome formation in magnetotactic bacteria. IMPORTANCE Magnetotactic bacteria synthesize magnetite (Fe3O4) nanocrystals in a prokaryotic organelle called the magnetosome. This organelle is formed using various magnetosome proteins in multiple steps, including vesicle formation, magnetosome alignment, and magnetite crystal formation, to provide compartmentalized nanospaces for the regulation of iron concentrations and redox conditions, enabling the synthesis of a morphologically controlled magnetite crystal. Thus, to rationalize the complex organelle development, the localization of magnetosome proteins is considered to be highly regulated; however, the mechanisms remain largely unknown. Here, we performed comparative localization analysis of magnetosome proteins that revealed the presence of a spatial regulation mechanism within the linear structure of magnetosomes. This discovery provides evidence of a highly regulated protein localization mechanism for this bacterial organelle development.
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194
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Giessen TW, Silver PA. A Catalytic Nanoreactor Based on in Vivo Encapsulation of Multiple Enzymes in an Engineered Protein Nanocompartment. Chembiochem 2016; 17:1931-1935. [DOI: 10.1002/cbic.201600431] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Tobias W. Giessen
- Department of Systems Biology; Harvard Medical School; 200 Longwood Avenue WAB 536 Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; 3 Blackfan Circle Boston MA 02115 USA
| | - Pamela A. Silver
- Department of Systems Biology; Harvard Medical School; 200 Longwood Avenue WAB 536 Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; 3 Blackfan Circle Boston MA 02115 USA
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195
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Prioretti L, Lebrun R, Gontero B, Giordano M. Redox regulation of ATP sulfurylase in microalgae. Biochem Biophys Res Commun 2016; 478:1555-62. [PMID: 27613093 DOI: 10.1016/j.bbrc.2016.08.151] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 01/29/2023]
Abstract
ATP sulfurylase (ATPS) catalyzes the first step of sulfur assimilation in photosynthetic organisms. An ATPS type A is mostly present in freshwater cyanobacteria, with four conserved cysteine residues. Oceanic cyanobacteria and most eukaryotic algae instead, possess an ATPS-B containing seven to ten cysteines; five of them are conserved, but only one in the same position as ATPS-A. We investigated the role of cysteines on the regulation of the different algal enzymes. We found that the activity of ATPS-B from four different microorganisms was enhanced when reduced and decreased when oxidized. The LC-MS/MS analysis of the ATPS-B from the marine diatom Thalassiosira pseudonana showed that the residue Cys-247 was presumably involved in the redox regulation. The absence of this residue in the ATPS-A of the freshwater cyanobacterium Synechocystis sp. instead, was consistent with its lack of regulation. Some other conserved cysteine residues in the ATPS from T. pseduonana and not in Synechocystis sp.were accessible to redox agents and possibly play a role in the enzyme regulation. Furthermore, the fact that oceanic cyanobacteria have ATPS-B structurally and functionally closer to that from most of eukaryotic algae than to the ATPS-A from other cyanobacteria suggests that life in the sea or freshwater may have driven the evolution of ATPS.
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Affiliation(s)
- Laura Prioretti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy; Aix Marseille Univ, CNRS, BIP UMR 7281, IMM, 31 Chemin J. Aiguier, 13402 Marseille Cedex 20, France
| | - Régine Lebrun
- Plate-forme Protéomique, MaP, IMM, FR 3479, CNRS, 31 Chemin J. Aiguier, 13402 Marseille Cedex 20, France
| | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP UMR 7281, IMM, 31 Chemin J. Aiguier, 13402 Marseille Cedex 20, France
| | - Mario Giordano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy; Institute of Microbiology ASCR, Algatech, Trebon, Czech Republic; National Research Council, Institute of Marine Science, Venezia, Italy.
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196
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Chowdhury C, Chun S, Sawaya MR, Yeates TO, Bobik TA. The function of the PduJ microcompartment shell protein is determined by the genomic position of its encoding gene. Mol Microbiol 2016; 101:770-83. [PMID: 27561553 PMCID: PMC5003431 DOI: 10.1111/mmi.13423] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2016] [Indexed: 12/20/2022]
Abstract
Bacterial microcompartments (MCPs) are complex organelles that consist of metabolic enzymes encapsulated within a protein shell. In this study, we investigate the function of the PduJ MCP shell protein. PduJ is 80% identical in amino acid sequence to PduA and both are major shell proteins of the 1,2-propanediol (1,2-PD) utilization (Pdu) MCP of Salmonella. Prior studies showed that PduA mediates the transport of 1,2-PD (the substrate) into the Pdu MCP. Surprisingly, however, results presented here establish that PduJ has no role 1,2-PD transport. The crystal structure revealed that PduJ was nearly identical to that of PduA and, hence, offered no explanation for their differential functions. Interestingly, however, when a pduJ gene was placed at the pduA chromosomal locus, the PduJ protein acquired a new function, the ability to mediate 1,2-PD transport into the Pdu MCP. To our knowledge, these are the first studies to show that that gene location can determine the function of a MCP shell protein. We propose that gene location dictates protein-protein interactions essential to the function of the MCP shell.
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Affiliation(s)
- Chiranjit Chowdhury
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
| | - Sunny Chun
- Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095
| | - Michael R. Sawaya
- Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095
| | - Todd O. Yeates
- Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
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197
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pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism. Proc Natl Acad Sci U S A 2016; 113:E5354-62. [PMID: 27551079 DOI: 10.1073/pnas.1525145113] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Many carbon-fixing bacteria rely on a CO2 concentrating mechanism (CCM) to elevate the CO2 concentration around the carboxylating enzyme ribulose bisphosphate carboxylase/oxygenase (RuBisCO). The CCM is postulated to simultaneously enhance the rate of carboxylation and minimize oxygenation, a competitive reaction with O2 also catalyzed by RuBisCO. To achieve this effect, the CCM combines two features: active transport of inorganic carbon into the cell and colocalization of carbonic anhydrase and RuBisCO inside proteinaceous microcompartments called carboxysomes. Understanding the significance of the various CCM components requires reconciling biochemical intuition with a quantitative description of the system. To this end, we have developed a mathematical model of the CCM to analyze its energetic costs and the inherent intertwining of physiology and pH. We find that intracellular pH greatly affects the cost of inorganic carbon accumulation. At low pH the inorganic carbon pool contains more of the highly cell-permeable H2CO3, necessitating a substantial expenditure of energy on transport to maintain internal inorganic carbon levels. An intracellular pH ≈8 reduces leakage, making the CCM significantly more energetically efficient. This pH prediction coincides well with our measurement of intracellular pH in a model cyanobacterium. We also demonstrate that CO2 retention in the carboxysome is necessary, whereas selective uptake of HCO3 (-) into the carboxysome would not appreciably enhance energetic efficiency. Altogether, integration of pH produces a model that is quantitatively consistent with cyanobacterial physiology, emphasizing that pH cannot be neglected when describing biological systems interacting with inorganic carbon pools.
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198
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The two Dps proteins, NpDps2 and NpDps5, are involved in light-induced oxidative stress tolerance in the N 2-fixing cyanobacterium Nostoc punctiforme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1766-1776. [PMID: 27528559 DOI: 10.1016/j.bbabio.2016.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/09/2016] [Accepted: 08/11/2016] [Indexed: 11/23/2022]
Abstract
Cyanobacteria are photosynthetic prokaryotes that are considered biotechnologically prominent organisms for production of high-value compounds. Cyanobacteria are subject to high-light intensities, which is a challenge that needs to be addressed in design of efficient bio-engineered photosynthetic organisms. Dps proteins are members of the ferritin superfamily and are omnipresent in prokaryotes. They play a major role in oxidative stress protection and iron homeostasis. The filamentous, heterocyst-forming Nostoc punctiforme, has five Dps proteins. In this study we elucidated the role of these Dps proteins in acclimation to high light intensity, the gene loci organization and the transcriptional regulation of all five dps genes in N. punctiforme was revealed, and dps-deletion mutant strains were used in physiological characterization. Two mutants defective in Dps2 and Dps5 activity displayed a reduced fitness under increased illumination, as well as a differential Photosystem (PS) stoichiometry, with an elevated Photosystem II to Photosystem I ratio in the dps5 deletion strain. This work establishes a Dps-mediated link between light tolerance, H2O2 detoxification, and iron homeostasis, and provides further evidence on the non-redundant role of multiple Dps proteins in this multicellular cyanobacterium.
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199
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Frey R, Mantri S, Rocca M, Hilvert D. Bottom-up Construction of a Primordial Carboxysome Mimic. J Am Chem Soc 2016; 138:10072-5. [DOI: 10.1021/jacs.6b04744] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Raphael Frey
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Shiksha Mantri
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Marco Rocca
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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200
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Polka JK, Hays SG, Silver PA. Building Spatial Synthetic Biology with Compartments, Scaffolds, and Communities. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a024018. [PMID: 27270297 DOI: 10.1101/cshperspect.a024018] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Traditional views of synthetic biology often treat the cell as an unstructured container in which biological reactions proceed uniformly. In reality, the organization of biological molecules has profound effects on cellular function: not only metabolic, but also physical and mechanical. Here, we discuss a variety of perturbations available to biologists in controlling protein, nucleotide, and membrane localization. These range from simple tags, fusions, and scaffolds to heterologous expression of compartments and other structures that confer unique physical properties to cells. Next, we relate these principles to those guiding the spatial environments outside of cells such as the extracellular matrix. Finally, we discuss new directions in building intercellular organizations to create novel symbioses.
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Affiliation(s)
- Jessica K Polka
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115
| | - Stephanie G Hays
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115 Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115
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