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1. Role of carboxysomes in cyanobacterial CO2 assimilation: CO2 concentrating mechanisms and metabolon implications

   https://doi.org/10.1111/1462-2920.16283  

   Huffine, Clair A. ; Zhao, Runyu ; Tang, Yinjie J. ; Cameron, Jeffrey C. ( November 2022 , Environmental Microbiology)

   Many carbon‐fixing organisms have evolved CO₂concentrating mechanisms (CCMs) to enhance the delivery of CO₂to RuBisCO, while minimizing reactions with the competitive inhibitor, molecular O₂. These distinct types of CCMs have been extensively studied using genetics, biochemistry, cell imaging, mass spectrometry, and metabolic flux analysis. Highlighted in this paper, the cyanobacterial CCM features a bacterial microcompartment (BMC) called ‘carboxysome’ in which RuBisCO is co‐encapsulated with the enzyme carbonic anhydrase (CA) within a semi‐permeable protein shell. The cyanobacterial CCM is capable of increasing CO₂around RuBisCO, leading to one of the most efficient processes known for fixing ambient CO₂. The carboxysome life cycle is dynamic and creates a unique subcellular environment that promotes activity of the Calvin–Benson (CB) cycle. The carboxysome may function within a larger cellular metabolon, physical association of functionally coupled proteins, to enhance metabolite channelling and carbon flux. In light of CCMs, synthetic biology approaches have been used to improve enzyme complex for CO₂fixations. Research on CCM‐associated metabolons has also inspired biologists to engineer multi‐step pathways by providing anchoring points for enzyme cascades to channel intermediate metabolites towards valuable products.

    

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2. Carbon‐concentrating mechanisms are a key trait in lichen ecology and distribution

   https://doi.org/10.1002/ecy.4011  

   Koch, Natália M. ; Lendemer, James C. ; Manzitto‐Tripp, Erin A. ; McCain, Christy ; Stanton, Daniel E. ( March 2023 , Ecology)

   Carbon‐concentrating mechanisms (CCMs) are a widespread phenomenon in photosynthetic organisms. In vascular plants, the evolution of CCMs ([C44‐carbon compound] and crassulacean acid metabolism [CAM]) is associated with significant shifts, most often to hot, dry and bright, or aquatic environments. If and how CCMs drive distributions of other terrestrial photosynthetic organisms, remains little studied. Lichens are ecologically important obligate symbioses between fungi and photosynthetic organisms. The primary photosynthetic partner in these symbioses can include CCM‐presenting cyanobacteria (as carboxysomes), CCM‐presenting green algae (as pyrenoids) or green algae lacking any CCM. We use an extensive dataset of lichen communities from eastern North America, spanning a wide climatic range, to test the importance of CCMs as predictors of lichen ecology and distribution. We show that the presence or absence of CCMs leads to opposite responses to temperature and precipitation in green algal lichens, and different responses in cyanobacterial lichens. These responses contrast with our understanding of lichen physiology, whereby CCMs mitigate carbon limitation by water saturation at the cost of efficient use of vapor hydration. This study demonstrates that CCM status is a key functional trait in obligate lichen symbioses, equivalent in importance to its role in vascular plants, and central for studying present and future climate responses.

    

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3. LCI1, a Chlamydomonas reinhardtii plasma membrane protein, functions in active CO 2 uptake under low CO 2

   https://doi.org/10.1111/tpj.14761  

   Kono, Alfredo ; Spalding, Martin H. ( April 2020 , The Plant Journal)

   In response to high CO₂environmental variability, green algae, such asChlamydomonas reinhardtii, have evolved multiple physiological states dictated by external CO₂concentration. Genetic and physiological studies demonstrated that at least three CO₂physiological states, a high CO₂(0.5–5% CO₂), a low CO₂(0.03–0.4% CO₂) and a very low CO₂(< 0.02% CO₂) state, exist inChlamydomonas. To acclimate in the low and very low CO₂states,Chlamydomonasinduces a sophisticated strategy known as a CO₂‐concentrating mechanism (CCM) that enables proliferation and survival in these unfavorable CO₂environments. Active uptake of C_ifrom the environment is a fundamental aspect in theChlamydomonasCCM, and consists of CO₂and HCO₃^–uptake systems that play distinct roles in low and very low CO₂acclimation states. LCI1, a putative plasma membrane C_itransporter, has been linked through conditional overexpression to active C_iuptake. However, both the role of LCI1 in various CO₂acclimation states and the species of C_i, HCO₃^–or CO₂, that LCI1 transports remain obscure. Here we report the impact of anLCI1loss‐of‐function mutant on growth and photosynthesis in different genetic backgrounds at multiple pH values. These studies show that LCI1 appears to be associated with active CO₂uptake in low CO₂, especially above air‐level CO₂, and that any LCI1 role in very low CO₂is minimal.

    

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4. Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H

   https://doi.org/10.1073/pnas.1807804115  

   Czajka, Jeffrey J. ; Abernathy, Mary H. ; Benites, Veronica T. ; Baidoo, Edward E. K. ; Deming, Jody W. ; Tang, Yinjie J. ( November 2018 , Proceedings of the National Academy of Sciences)

   Colwellia psychrerythraea34H is a model psychrophilic bacterium found in the cold ocean—polar sediments, sea ice, and the deep sea. Although the genomes of such psychrophiles have been sequenced, their metabolic strategies at low temperature have not been quantified. We measured the metabolic fluxes and gene expression of 34H at 4 °C (the mean global-ocean temperature and a normal-growth temperature for 34H), making comparative analyses at room temperature (above its upper-growth temperature of 18 °C) and with mesophilicEscherichia coli. When grown at 4 °C, 34H utilized multiple carbon substrates without catabolite repression or overflow byproducts; its anaplerotic pathways increased flux network flexibility and enabled CO₂fixation. In glucose-only medium, the Entner–Doudoroff (ED) pathway was the primary glycolytic route; in lactate-only medium, gluconeogenesis and the glyoxylate shunt became active. In comparison,E. coli, cold stressed at 4 °C, had rapid glycolytic fluxes but no biomass synthesis. At their respective normal-growth temperatures, intracellular concentrations of TCA cycle metabolites (α-ketoglutarate, succinate, malate) were 4–17 times higher in 34H than inE. coli, while levels of energy molecules (ATP, NADH, NADPH) were 10- to 100-fold lower. Experiments withE. colimutants supported the thermodynamic advantage of the ED pathway at cold temperature. Heat-stressed 34H at room temperature (2 hours) revealed significant down-regulation of genes associated with glycolytic enzymes and flagella, while 24 hours at room temperature caused irreversible cellular damage. We suggest that marine heterotrophic bacteria in general may rely upon simplified metabolic strategies to overcome thermodynamic constraints and thrive in the cold ocean.

    

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5. Dissolved inorganic carbon accumulating complexes from autotrophic bacteria from extreme environments

   https://doi.org/10.1128/JB.00377-21  

   Schmid, Sarah ; Chaput, Dale ; Breitbart, Mya ; Hines, Rebecca ; Williams, Samantha ; Gossett, Hunter K. ; Parsi, Sheila D. ; Peterson, Rebecca ; Whittaker, Robert A. ; Tarver, Angela ; et al ( September 2021 , Journal of Bacteriology)

   null (Ed.)

   In nature, concentrations of dissolved inorganic carbon (DIC; = CO 2 + HCO 3 - + CO 3 2- ) can be low, and autotrophic organisms adapt with a variety of mechanisms to elevate intracellular DIC concentrations to enhance CO 2 fixation. Such mechanisms have been well-studied in Cyanobacteria , but much remains to be learned about their activity in other phyla. Novel multi-subunit membrane-spanning complexes capable of elevating intracellular DIC were recently described in three species of bacteria. Homologs of these complexes are distributed among 17 phyla in Bacteria and Archaea, and are predicted to consist of one, two, or three subunits. To determine whether DIC accumulation is a shared feature of these diverse complexes, seven of them, representative of organisms from four phyla, from a variety of habitats, and with three different subunit configurations were chosen for study. A high-CO 2 requiring, carbonic anhydrase-deficient ( yadF - cynT - ) strain of E. coli Lemo21(DE3), which could be rescued via elevated intracellular DIC concentrations, was created for heterologous expression and characterization of the complexes. Expression of all seven complexes rescued the ability of E. coli Lemo21(DE3) yadF - cynT - to grow under low CO 2 conditions, and six of the seven generated measurably elevated intracellular DIC concentrations when their expression was induced. For complexes consisting of two or three subunits, all subunits were necessary for DIC accumulation. Isotopic disequilibrium experiments clarified that CO 2 was the substrate for these complexes. In addition, the presence of an ionophore prevented the accumulation of intracellular DIC, suggesting that these complexes may couple proton potential to DIC accumulation. IMPORTANCE To facilitate the synthesis of biomass from CO 2 , autotrophic organisms use a variety of mechanisms to increase intracellular DIC concentrations. A novel type of multi-subunit complex has recently been described, which has been shown to generate measurably elevated intracellular DIC concentrations in three species of bacteria, begging the question of whether these complexes share this capability across the 17 phyla of Bacteria and Archaea where they are found. This study shows that DIC accumulation is a trait shared by complexes with varied subunit structures, from organisms with diverse physiologies and taxonomies, suggesting that this trait is universal among them. Successful expression in E. coli suggests the possibility of their expression in engineered organisms synthesizing compounds of industrial importance from CO 2 . 

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