The CO2-concentrating mechanism of cyanobacteria and evolution by horizontal gene transfer

Abstract

Using a wide range of physiological, bioinformatic and molecular techniques, the contribution of horizontal gene transfer (HGT) to the carbon dioxide-concentrating mechanism (CCM) of cyanobacteria was investigated. The CCM allows cyanobacteria to survive in sub-saturating carbon-dioxide conditions. The carboxysome, which contains most of the RuBisCO in cyanobacterial cells, is a central feature of the CCM. Two types of carboxysome exist, and these are characteristic of two monophyletic groups called alpha and beta-cyanobacteria. Different phylogenetic groups of cyanobacteria have characteristic Ci-uptake systems, which accumulate Ci as a cytoplasmic bicarbonate pool. Within the carboxysome, carbonic anhydrase (CA) converts this bicarbonate to carbon-dioxide near to the site where it is fixed into carbohydrates by RuBisCO.

Bioinformatic analysis showed that a group of oceanic a-cyanobacteria called Cyanobium had gained beta-cyanobacterial Ci-uptake systems, potentially as an adaptive process in transition from an oceanic to a fresh/brackish water habitat. The expression and contribution of these transporters, SbtAl, SbtA2 and NDH-I3, to the physiological CCM of Cyanobium was investigated, revealing the strong likelihood that whilst these species had gained foreign Ci-uptake systems by HGT, some strains could not regulate their transcription in the canonical pattern. Nonetheless, the effect of HGT on adaptation to environments with fluctuating Ci was clear.

The beta-carboxysome has a complex structure, and its components are encoded by the ccm operon. The carboxysomal contribution of putative shell proteins from the ccm and other operons was investigated in Synechococcus elongatus PCC 7942. This showed specific structural roles for different proteins. CcmK2 and CcmO were the major outer shell proteins, and CcmK3 and CcmK4 were minor. The possibility of a specific pore for the RuBisCO substrate RuBP was discussed, and there was some evidence that CcmK3 and CcmK4 were involved in this process. Whilst the structure of the beta-carboxysome could be formed from RuBisCO and the ccmK-O operon, the carboxysomes were not fully functional until at least the carboxysomal CA and one accessory shell protein were present. It was evident that HGT of an ancestral operon, ccmKLMNO, could have been responsible for the wide distribution of {u03B2}-carboxysomes in cyanobacteria containing form-IB RuBisCO.

The most important structural protein in the beta-carboxysome is CcmM, which has two isoforms with distinct structural roles. The potential for HGT of this structural, and potentially enzymatic, protein was investigated by transgenic expression of foreign ccmM genes in the {u25B3}ccmM mutant of S.elongatus PCC 7942. Whilst the foreign genes could produce both CcmM isoforms in the new host, only ccmM from Synechococcus PCC 7002 could form physiologically relevant carboxysome-like structures. Nonetheless, these structures were predicted to be evolutionarily relevant, and could, perhaps, evolve into effective carboxysomes over time. These results suggested an evolutionary trajectory that lead to the contemporary {u03B2}-carboxysome.

The principle of HGT pervades the cyanobacterial CCM. Both types of carboxysome, as well as the Ci uptake systems of many cyanobacterial species, appear to have undergone HGT at some point. Thus, as shown in other bacterial systems, HGT allows the rare innovations of a few individuals to benefit widely dispersed and heterologous bacteria. Show more