Bioinformatic analysis of the distribution of inorganic carbon transporters and prospective targets for bioengineering to increase Ci uptake by cyanobacteria.
Cyanobacteria have evolved a carbon-concentrating mechanism (CCM) which has enabled them to inhabit diverse environments encompassing a range of inorganic carbon (Ci: [Formula: see text] and CO2) concentrations. Several uptake systems facilitate inorganic carbon accumulation in the cell, which can in turn be fixed by ribulose 1,5-bisphosphate carboxylase/oxygenase. Here we survey the distribution of genes encoding known Ci uptake systems in cyanobacterial genomes and, using a pfam- and gene context-based approach, identify in the marine (alpha) cyanobacteria a heretofore unrecognized number of putative counterparts to the well-known Ci transporters of beta cyanobacteria. In addition, our analysis shows that there is a huge repertoire of transport systems in cyanobacteria of unknown function, many with homology to characterized Ci transporters. These can be viewed as prospective targets for conversion into ancillary Ci transporters through bioengineering. Increasing intracellular Ci concentration coupled with efforts to increase carbon fixation will be beneficial for the downstream conversion of fixed carbon into value-added products including biofuels. In addition to CCM transporter homologs, we also survey the occurrence of rhodopsin homologs in cyanobacteria, including bacteriorhodopsin, a class of retinal-binding, light-activated proton pumps. Because they are light driven and because of the apparent ease of altering their ion selectivity, we use this as an example of re-purposing an endogenous transporter for the augmentation of Ci uptake by cyanobacteria and potentially chloroplasts.
DOE Plant Research Laboratories, Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA.
Sandeep B
SB
Gaudana
DOE Plant Research Laboratories, Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA.|Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Jan
J
Zarzycki
Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
Vamsi K
VK
Moparthi
DOE Plant Research Laboratories, Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA. ckerfeld@lbl.gov.|Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. ckerfeld@lbl.gov.|Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA. ckerfeld@lbl.gov.
Cheryl A
CA
Kerfeld
D001692:Biological Transport; D002244:Carbon / Q000378:metabolism*; D057486:Carbon Cycle; D019295:Computational Biology / Q000379:methods*; D000458:Cyanobacteria / Q000378:metabolism / Q000502:physiology*; D015964:Gene Expression Regulation, Bacterial; D005818:Genetic Engineering / Q000379:methods*; D008027:Light; D025604:Rhodopsins, Microbial / Q000235:genetics / Q000378:metabolism
D025604:Rhodopsins, Microbial; D002244:Carbon
Bioinformatics; Carbon fixation; Carbon-concentrating mechanism; Cyanobacteria; Genomic context; Inorganic carbon transport; Rhodopsin; Synthetic biology; pfam