Bioinformatic analysis of the distribution of inorganic carbon transporters and prospective targets for bioengineering to increase C sub(i) uptake by cyanobacteria

• Published in: Photosynthesis research Vol. 126; no. 1; pp. 99 - 109
• Main Authors: Gaudana, Sandeep B, Zarzycki, Jan, Moparthi, Vamsi K, Kerfeld, Cheryl A
• Format: Journal Article
• Language: English
• Published: 01.10.2015
• Subjects: Cyanobacteria
• ISSN: 0166-8595; 1573-5079
• DOI: 10.1007/s11120-014-0059-8

(ProQuest: ... denotes formulae and/or non-USASCII text omitted; see image).Cyanobacteria have evolved a carbon-concentrating mechanism (CCM) which has enabled them to inhabit diverse environments encompassing a range of inorganic carbon (C sub(i): ... and CO sub(2)) 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 C sub(i) 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 C sub(i) 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 C sub(i) transporters. These can be viewed as prospective targets for conversion into ancillary C sub(i) transporters through bioengineering. Increasing intracellular C sub(i) 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 C sub(i) uptake by cyanobacteria and potentially chloroplasts.