scholarly journals A Novel Evolutionary Lineage of Carbonic Anhydrase (ε Class) Is a Component of the Carboxysome Shell

2004 ◽  
Vol 186 (3) ◽  
pp. 623-630 ◽  
Author(s):  
Anthony K.-C. So ◽  
George S. Espie ◽  
Eric B. Williams ◽  
Jessup M. Shively ◽  
Sabine Heinhorst ◽  
...  
Keyword(s):  
Carbonic Anhydrase ◽  
Active Sites ◽  
Carbon Fixation ◽  
Total Carbon ◽  
Bisphosphate Carboxylase ◽  
Evolutionary Lineage ◽  
Shell Protein ◽  
Essential Components ◽  
Halothiobacillus Neapolitanus ◽  
Chemolithoautotrophic Bacteria

ABSTRACT A significant portion of the total carbon fixed in the biosphere is attributed to the autotrophic metabolism of prokaryotes. In cyanobacteria and many chemolithoautotrophic bacteria, CO2 fixation is catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), most if not all of which is packaged in protein microcompartments called carboxysomes. These structures play an integral role in a cellular CO2-concentrating mechanism and are essential components for autotrophic growth. Here we report that the carboxysomal shell protein, CsoS3, from Halothiobacillus neapolitanus is a novel carbonic anhydrase (ε-class CA) that has an evolutionary lineage distinct from those previously recognized in animals, plants, and other prokaryotes. Functional CAs encoded by csoS3 homologues were also identified in the cyanobacteria Prochlorococcus sp. and Synechococcus sp., which dominate the oligotrophic oceans and are major contributors to primary productivity. The location of the carboxysomal CA in the shell suggests that it could supply the active sites of RuBisCO in the carboxysome with the high concentrations of CO2 necessary for optimal RuBisCO activity and efficient carbon fixation in these prokaryotes, which are important contributors to the global carbon cycle.

scholarly journals Characterization of the Carboxysomal Carbonic Anhydrase CsoSCA from Halothiobacillus neapolitanus

2006 ◽  
Vol 188 (23) ◽  
pp. 8087-8094 ◽  
Author(s):  
Sabine Heinhorst ◽  
Eric B. Williams ◽  
Fei Cai ◽  
C. Daniel Murin ◽  
Jessup M. Shively ◽  
...  
Keyword(s):  
Carbonic Anhydrase ◽  
Catalytic Efficiency ◽  
Biochemical Properties ◽  
Bisphosphate Carboxylase ◽  
Shell Protein ◽  
Dehydration Reactions ◽  
Chemolithotrophic Bacteria ◽  
Halothiobacillus Neapolitanus ◽  
Protein Shell

ABSTRACT In cyanobacteria and many chemolithotrophic bacteria, the CO2-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is sequestered into polyhedral protein bodies called carboxysomes. The carboxysome is believed to function as a microcompartment that enhances the catalytic efficacy of RubisCO by providing the enzyme with its substrate, CO2, through the action of the shell protein CsoSCA, which is a novel carbonic anhydrase. In the work reported here, the biochemical properties of purified, recombinant CsoSCA were studied, and the catalytic characteristics of the carbonic anhydrase for the CO2 hydration and bicarbonate dehydration reactions were compared with those of intact and ruptured carboxysomes. The low apparent catalytic rates measured for CsoSCA in intact carboxysomes suggest that the protein shell acts as a barrier for the CO2 that has been produced by CsoSCA through directional dehydration of cytoplasmic bicarbonate. This CO2 trap provides the sequestered RubisCO with ample substrate for efficient fixation and constitutes a means by which microcompartmentalization enhances the catalytic efficiency of this enzyme.

scholarly journals Many-molecule encapsulation by an icosahedral shell

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Jason D Perlmutter ◽  
Farzaneh Mohajerani ◽  
Michael F Hagan
Keyword(s):  
Carbonic Anhydrase ◽  
Protein Interactions ◽  
Carbon Fixation ◽  
The Other ◽  
Control Parameters ◽  
Bisphosphate Carboxylase ◽  
Bacterial Microcompartment ◽  
Shell Proteins ◽  
Assembly Pathways

We computationally study how an icosahedral shell assembles around hundreds of molecules. Such a process occurs during the formation of the carboxysome, a bacterial microcompartment that assembles around many copies of the enzymes ribulose 1,5-bisphosphate carboxylase/ oxygenase and carbonic anhydrase to facilitate carbon fixation in cyanobacteria. Our simulations identify two classes of assembly pathways leading to encapsulation of many-molecule cargoes. In one, shell assembly proceeds concomitantly with cargo condensation. In the other, the cargo first forms a dense globule; then, shell proteins assemble around and bud from the condensed cargo complex. Although the model is simplified, the simulations predict intermediates and closure mechanisms not accessible in experiments, and show how assembly can be tuned between these two pathways by modulating protein interactions. In addition to elucidating assembly pathways and critical control parameters for microcompartment assembly, our results may guide the reengineering of viruses as nanoreactors that self-assemble around their reactants.

scholarly journals Superresolution microscopy of the β-carboxysome reveals a homogeneous matrix

2017 ◽  
Vol 28 (20) ◽  
pp. 2734-2745 ◽  
Author(s):  
Matthew J. Niederhuber ◽  
Talley J. Lambert ◽  
Clarence Yapp ◽  
Pamela A. Silver ◽  
Jessica K. Polka
Keyword(s):  
Carbon Fixation ◽  
Three Dimensional ◽  
Population Level ◽  
Automated Analysis ◽  
Time Lapse ◽  
Wide Field ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Bisphosphate Carboxylase ◽  
Shell Protein

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.

scholarly journals Decoding the absolute stoichiometric composition and structural plasticity of α-carboxysomes

2021 ◽  
Author(s):  
Yaqi Sun ◽  
Victoria M. Harman ◽  
James R. Johnson ◽  
Taiyu Chen ◽  
Gregory F. Dykes ◽  
...  
Keyword(s):  
Rational Design ◽  
Carbon Fixation ◽  
Stoichiometric Composition ◽  
Quantitative Mass Spectrometry ◽  
Shell Protein ◽  
Self Assembling ◽  
The Absolute ◽  
Halothiobacillus Neapolitanus ◽  
Protein Shell ◽  
Insight Into

AbstractCarboxysomes are anabolic bacterial microcompartments that play an essential role in carbon fixation in cyanobacteria and some chemoautotrophs. This self-assembling organelle encapsulates the key CO2-fixing enzymes, Rubisco, and carbonic anhydrase using a polyhedral protein shell that is constructed by hundreds of shell protein paralogs. The α-carboxysome from the chemoautotroph Halothiobacillus neapolitanus serves as a model system in fundamental studies and synthetic engineering of carboxysomes. Here we adopt a QconCAT-based quantitative mass spectrometry to determine the absolute stoichiometric composition of native α-carboxysomes from H. neapolitanus. We further performed an in-depth comparison of the protein stoichiometry of native and recombinant α-carboxysomes heterologously generated in Escherichia coli to evaluate the structural variability and remodeling of α-carboxysomes. Our results provide insight into the molecular principles that mediate carboxysome assembly, which may aid in rational design and reprogramming of carboxysomes in new contexts for biotechnological applications.

scholarly journals Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow)

2021 ◽  
Vol 9 (7) ◽  
pp. 1368
Author(s):  
Qianqian Li ◽  
Rebecca E. Cooper ◽  
Carl-Eric Wegner ◽  
Martin Taubert ◽  
Nico Jehmlich ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Co2 Fixation ◽  
Carbon Fixation ◽  
Stable Isotope Probing ◽  
Acidic Lake ◽  
General Role ◽  
Polysaccharide Biosynthesis ◽  
Iron Oxidizers ◽  
Metabolic Activities ◽  
Chemolithoautotrophic Bacteria

Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO2 fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace 13CO2 incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6–85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. 13CO2 incorporation studies identified active chemolithoautotroph Ferrovum under both conditions. Only 1.0–5.3% relative 13C abundances were found in heterotrophic Acidiphilium and Acidocella under oxic conditions. These data show that iron oxidizers play an important role in CO2 fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.

CARBONIC ANHYDRASE AND CARBON FIXATION IN COCCOLITHOPHORIDS

1982 ◽  
Vol 18 (3) ◽  
pp. 423-426 ◽  
Author(s):  
C. Steven Sikes ◽  
A. P. Wheeler
Keyword(s):  
Carbonic Anhydrase ◽  
Carbon Fixation

scholarly journals Whole-Genome Transcriptional Profiling of Bradyrhizobium japonicum during Chemoautotrophic Growth

2008 ◽  
Vol 190 (20) ◽  
pp. 6697-6705 ◽  
Author(s):  
William L. Franck ◽  
Woo-Suk Chang ◽  
Jing Qiu ◽  
Masayuki Sugawara ◽  
Michael J. Sadowsky ◽  
...  
Keyword(s):  
Bradyrhizobium Japonicum ◽  
Carbon Fixation ◽  
Cultured Cells ◽  
Isocitrate Lyase ◽  
Nitrogenase Activity ◽  
Glyoxylate Cycle ◽  
Transcriptional Profiling ◽  
Pentose Phosphate ◽  
Hydrogen Gas ◽  
Essential Components

ABSTRACT Bradyrhizobium japonicum is a facultative chemoautotroph capable of utilizing hydrogen gas as an electron donor in a respiratory chain terminated by oxygen to provide energy for cellular processes and carbon dioxide assimilation via a reductive pentose phosphate pathway. A transcriptomic analysis of B. japonicum cultured chemoautotrophically identified 1,485 transcripts, representing 17.5% of the genome, as differentially expressed when compared to heterotrophic cultures. Genetic determinants required for hydrogen utilization and carbon fixation, including the uptake hydrogenase system and components of the Calvin-Benson-Bassham cycle, were strongly induced in chemoautotrophically cultured cells. A putative isocitrate lyase (aceA; blr2455) was among the most strongly upregulated genes, suggesting a role for the glyoxylate cycle during chemoautotrophic growth. Addition of arabinose to chemoautotrophic cultures of B. japonicum did not significantly alter transcript profiles. Furthermore, a subset of nitrogen fixation genes was moderately induced during chemoautotrophic growth. In order to specifically address the role of isocitrate lyase and nitrogenase in chemoautotrophic growth, we cultured aceA, nifD, and nifH mutants under chemoautotrophic conditions. Growth of each mutant was similar to that of the wild type, indicating that the glyoxylate bypass and nitrogenase activity are not essential components of chemoautotrophy in B. japonicum.

scholarly journals Design and in vitro realization of carbon-conserving photorespiration

2018 ◽  
Vol 115 (49) ◽  
pp. E11455-E11464 ◽  
Author(s):  
Devin L. Trudeau ◽  
Christian Edlich-Muth ◽  
Jan Zarzycki ◽  
Marieke Scheffen ◽  
Moshe Goldsmith ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Calvin Cycle ◽  
Computational Design ◽  
Carbon Loss ◽  
Fixation Rate ◽  
Bisphosphate Carboxylase ◽  
Stoichiometric Model ◽  
Synthetic Routes ◽  
Coa Reductase

Photorespiration recycles ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenation product, 2-phosphoglycolate, back into the Calvin Cycle. Natural photorespiration, however, limits agricultural productivity by dissipating energy and releasing CO2. Several photorespiration bypasses have been previously suggested but were limited to existing enzymes and pathways that release CO2. Here, we harness the power of enzyme and metabolic engineering to establish synthetic routes that bypass photorespiration without CO2 release. By defining specific reaction rules, we systematically identified promising routes that assimilate 2-phosphoglycolate into the Calvin Cycle without carbon loss. We further developed a kinetic–stoichiometric model that indicates that the identified synthetic shunts could potentially enhance carbon fixation rate across the physiological range of irradiation and CO2, even if most of their enzymes operate at a tenth of Rubisco’s maximal carboxylation activity. Glycolate reduction to glycolaldehyde is essential for several of the synthetic shunts but is not known to occur naturally. We, therefore, used computational design and directed evolution to establish this activity in two sequential reactions. An acetyl-CoA synthetase was engineered for higher stability and glycolyl-CoA synthesis. A propionyl-CoA reductase was engineered for higher selectivity for glycolyl-CoA and for use of NADPH over NAD+, thereby favoring reduction over oxidation. The engineered glycolate reduction module was then combined with downstream condensation and assimilation of glycolaldehyde to ribulose 1,5-bisphosphate, thus providing proof of principle for a carbon-conserving photorespiration pathway.

A simple dynamic model of photosynthesis in oak leaves: coupling leaf conductance and photosynthetic carbon fixation by a variable intracellular CO2 pool

2004 ◽  
Vol 31 (12) ◽  
pp. 1195 ◽  
Author(s):  
Steffen M. Noe ◽  
Christoph Giersch
Keyword(s):  
Carbon Fixation ◽  
Calvin Cycle ◽  
Target Function ◽  
Vapour Pressure Deficit ◽  
Co2 Assimilation ◽  
Leaf Conductance ◽  
Co2 Partial Pressure ◽  
Sink Term ◽  
Essential Components ◽  
Oak Leaves

Modelling the diurnal course of photosynthesis in oak leaves (Quercus robur L.) requires appropriate description of the dynamics of leaf photosynthesis of which diurnal variations in leaf conductance and in CO2 assimilation are essential components. We propose and analyse a simple photosynthesis model with three variables: leaf conductance (gs), the CO2 partial pressure inside the leaf (pi), and a pool of Calvin cycle intermediates (aps). The environmental factors light (I) and vapour pressure deficit (VPD) are used to formulate a target function G(I, VPD) from which the actual leaf conductance is calculated. Using this gs value and a CO2 consumption term representing CO2 fixation, a differential equation for pi is derived. Carboxylation corresponds to the sink term of the pi pool and is assumed to be feedback-inhibited by aps. This simple model is shown to produce reasonable to excellent fits to data on the diurnal time courses of photosythesis, pi and gs sampled for oak leaves.

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