An official website of the United States government
Cyanobacteria are responsible for up to 80% of aquatic carbon dioxide fixation and have evolved specialized carbon concentrating mechanism to increase photosynthetic yield. As such, cyanobacteria are attractive targets for synethic biology and engineering approaches to address the demands of global energy security, food production, and climate change for an increasing world’s population. The bicarbonate transporter BicA is a sodium-dependent, low-affinity, high-flux bicarbonate symporter expressed in the plasma membrane of cyanobacteria. Despite extensive biochemical characterization of BicA, including the resolution of the BicA crystal structure, the dynamic understanding of the bicarbonate mechanism remains elusive. To this end, we have collected over 1 ms of all-atom molecular dynamics simulation data of the BicA dimer to elucidate the structural rearrangements involved in the substrate transport process. We further characterized the energetics of the cooperativity between BicA promoters and investigated potential mutations that are shown to decrease the free energy barrier of conformational transitions. In all, our study illuminates a detailed mechanistic understanding of the conformational dynamics of bicarbonate transporters and provide atomistic insights to engineering these transporters for enhanced photosynthetic production.
more »
« less
This content will become publicly available on January 1, 2026
Molecular insights into the elevator-type mechanism of the cyanobacterial bicarbonate transporter BicA
Cyanobacteria are responsible for up to 80% of aquatic carbon dioxide fixation and have evolved a specialized carbon concentrating mechanism to increase photosynthetic yield. As such, cyanobacteria are attractive targets for synthetic biology and engineering approaches to address the demands of global energy security, food production, and climate change for an increasing world’s population. The bicarbonate transporter BicA is a sodium-dependent, low-affinity, high-flux bicarbonate symporter expressed in the plasma membrane of cyanobacteria. Despite extensive biochemical characterization of BicA, including the resolution of the BicA crystal structure, the dynamic understanding of the bicarbonate transport mechanism remains elusive. To this end, we have collected over 1 ms of all-atom molecular dynamics simulation data of the BicA dimer to elucidate the structural rearrangements involved in the substrate transport process. We further characterized the energetics of the transition of BicA protomers and investigated potential mutations that are shown to decrease the free energy barrier of conformational transitions. In all, our study illuminates a detailed mechanistic understanding of the conformational dynamics of bicarbonate transporters and provides atomistic insights to engineering these transporters for enhanced photosynthetic production.
more »
« less
- Award ID(s):
- 1845606
- PAR ID:
- 10587135
- Publisher / Repository:
- Biophysical Society
- Date Published:
- Journal Name:
- Biophysical Journal
- Volume:
- 124
- Issue:
- 2
- ISSN:
- 0006-3495
- Page Range / eLocation ID:
- 379 to 392
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
ABSTRACT Autotrophic microorganisms catalyze the entry of dissolved inorganic carbon (DIC; = CO2 + HCO3− + CO32−) into the biological component of the global carbon cycle, despite dramatic differences in DIC abundance and composition in their sometimes extreme environments. “Cyanobacteria” are known to have CO2 concentrating mechanisms (CCMs) to facilitate growth under low CO2 conditions. These CCMs consist of carboxysomes, containing enzymes ribulose 1,5-bisphosphate oxygenase and carbonic anhydrase, partnered to DIC transporters. CCMs and their DIC transporters have been studied in a handful of other prokaryotes, but it was not known how common CCMs were beyond “Cyanobacteria”. Since it had previously been noted that genes encoding potential transporters were found neighboring carboxysome loci, α-carboxysome loci were gathered from bacterial genomes, and potential transporter genes neighboring these loci are described here. Members of transporter families whose members all transport DIC (CHC, MDT and Sbt) were common in these neighborhoods, as were members of the SulP transporter family, many of which transport DIC. 109 of 115 taxa with carboxysome loci have some form of DIC transporter encoded in their genomes, suggesting that CCMs consisting of carboxysomes and DIC transporters are widespread not only among “Cyanobacteria”, but also among members of “Proteobacteria” and “Actinobacteria”.more » « less
-
Membrane transporters of the solute carrier 6 (SLC6) family mediate various physiological processes by facilitating the translocation of amino acids, neurotransmitters, and other metabolites. In the body, the activity of these transporters is tightly controlled through various post-translational modifications with implications on protein expression, stability, membrane trafficking, and dynamics. While N-linked glycosylation is a universal regulatory mechanism among eukaryotes, a consistent mechanism of how glycosylation affects the SLC6 transporter family remains elusive. It is generally believed that glycans influence transporter stability and membrane trafficking; however, the role of glycosylation on transporter dynamics remains disputable, with differing conclusions among individual transporters across the SLC6 family. In this study, we collected over 1 ms of aggregated all-atom molecular dynamics (MD) simulation data to systematically identify the impact of N-glycans on SLC6 transporter dynamics. We modeled four human SLC6 transporters, the serotonin, dopamine, glycine, and B0AT1 transporters, by first simulating all possible combinations of a glycan attached to each glycosylation site followed by investigating the effect of larger, oligo-N-linked glycans to each transporter. The simulations reveal that glycosylation does not significantly affect the transporter structure but alters the dynamics of the glycosylated extracellular loop and surrounding regions. The structural consequences of glycosylation on the loop dynamics are further emphasized with larger glycan molecules attached. However, no apparent differences in ligand stability or movement of the gating helices were observed, and as such, the simulations suggest that glycosylation does not have a profound effect on conformational dynamics associated with substrate transport.more » « less
-
IntroductionDeveloping sustainable hydrogen production is critical for advancing renewable energy and reducing reliance on fossil fuels. Cyanobacteria, which harness solar energy through photosynthesis, provide a promising biological platform for hydrogen generation. However, improving hydrogen yields requires strategic metabolic and genetic modifications to optimize energy flow and overcome photosynthetic limitations. MethodsFour cyanobacterial species were evaluated for their hydrogen production capacities under varying experimental conditions. Photosynthesis was partially inhibited using distinct chemical inhibitors, including 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). Exogenous glycerol was introduced as a supplementary carbon source. Hydrogen production was monitored over time, and rates were normalized to chlorophyll a content. Genomic analysis of transporter proteins was conducted to identify potential genetic loci for further enhancement of hydrogen output. ResultsNitrogen-fixingDolichospermumsp. exhibited significantly higher hydrogen production compared to the other tested species. Supplementation with glycerol notably increased both the rate and duration of hydrogen evolution, far exceeding previously established benchmarks. The maximum hydrogen production rate forDolichospermumsp. reached 132.3 μmol H₂/mg Chl a/h—representing a 30-fold enhancement over the rates observed with DCMU. Genomic screening revealed key transporter proteins with putative roles in carbon uptake and hydrogen metabolism. DiscussionThese findings underscore the potential of cyanobacteria, particularlyDolichospermumsp., as robust platforms for sustainable hydrogen production. The substantial improvements in hydrogen yield highlight the importance of targeted metabolic engineering and carbon supplementation strategies. Future work focused on optimizing identified transporter proteins and refining genetic interventions could further enhance biohydrogen efficiency. By leveraging the inherent photosynthetic machinery of cyanobacteria, this platform offers a renewable hydrogen source with significant promise for global energy sustainability.more » « less
-
Although cyanobacteria and algae represent a small fraction of the biomass of all primary producers, their photosynthetic activity accounts for roughly half of the daily CO2 fixation that occurs on Earth. These microorganisms are able to accomplish this feat by enhancing the activity of the CO2-fixing enzyme Rubisco using biophysical CO2 concentrating mechanisms (CCMs). Biophysical CCMs operate by concentrating bicarbonate and converting it into CO2 in a compartment that houses Rubisco (in contrast with other CCMs that concentrate CO2 via an organic intermediate, such as malate in the case of C4 CCMs). This activity provides Rubisco with a high concentration of its substrate, thereby increasing its reaction rate. The genetic engineering of a biophysical CCM into land plants is being pursued as a strategy to increase crop yields. This review focuses on the progress toward understanding the molecular components of cyanobacterial and algal CCMs, as well as recent advances toward engineering these components into land plants.more » « less
