Horizontal gene transfer from gammaproteobacteria to cyanobacteria and others

It seems to me that Gammaproteobacteria can transfer a lot of their photosynthesis related genes to other bacteria.

Recent phylogenetic studies (Bryant and Liu, 2013; Sousa et al., 2013) showed that an ancestor of marine Synechococcus and Prochlorococcus strains obtained a set of bchLNB genes from gammaproteobacteria. Such an event of lateral gene transfer from a gammaproteobacterium into an ancestor of the Synechococcus/Prochlorococcus group also included other genes, encoding proteins such as CmpA involved in circadian output (Dvornyk, 2006), carboxisome proteins, rubisco (Marin et al., 2007), threonyl tRNA synthetase, and quite possibly many more (Zhaxybayeva et al., 2006; Zhaxybayeva et al., 2009).

Gemmatimonas photoautotrophica acquired photosynthesis via horizontal gene transfer from a gammaproteobacterium (Zeng et al., 2014) and the same seems true for a Firmicutes of the genus Alkalibacterium. I wonder why...

Microbial mat

References
Bryant, D.A., and Liu, Z.F. (2013). Green bacteria: Insights into green bacterial evolution through genomic analyses. Advances in Botanical Research 66, 99-150.

Dvornyk, V. (2006). Subfamilies of cpmA, a gene involved in circadian output, have different evolutionary histories in cyanobacteria. Microbioliology 152, 75-84.

Marin, B., Nowack, E.C.M., Glockner, G., and Melkonian, M. (2007). The ancestor of the Paulinella chromatophore obtained a carboxysomal operon by horizontal gene transfer from a Nitrococcus-like gamma-proteobacterium. BMC evolutionary biology 7.

Perreault, N.N., Greer, C.W., Andersen, D.T., Tille, S., Lacrampe-Couloume, G., Lollar, B.S., and Whyte, L.G. (2008). Heterotrophic and autotrophic microbial populations in cold perennial springs of the high arctic. Appl. Environ. Microb. 74, 6898-6907.

Sousa, F.L., Shavit-Grievink, L., Allen, J.F., and Martin, W.F. (2013). Chlorophyll biosynthesis gene evolution indicates photosystem gene duplication, not photosystem merger, at the origin of oxygenic photosynthesis. Genome biology and evolution 5, 200-216.

Zeng, Y.H., Feng, F.Y., Medova, H., Dean, J., and Koblizek, M. (2014). Functional Type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes. P. Natl. Acad. Sci. U. S. A. 111, 7795-7800.

Zhaxybayeva, O., Doolittle, W.F., Papke, R.T., and Gogarten, J.P. (2009). Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus. Genome biology and evolution 1, 325-339.

Zhaxybayeva, O., Gogarten, J.P., Charlebois, R.L., Doolittle, W.F., and Papke, R.T. (2006). Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events. Genome Research 16, 1099-1108.

Evolution of oxygenic photosynthesis - New D1 sequences

Early this year I published a study on the evolution of all D1 proteins (Cardona et al., 2015). Interestingly, there are a number of sequences that were very atypical and appeared to be early evolving. Because of their phylogenetic position and sequence characteristics, I suggested that it is possible that these D1 sequences evolved before the water oxidizing complex had reached its standard configuration in PSII.

Back then there were about 40-45 atypical sequences. Since them more have appeared, there are a total of 62 sequences... so here I show a Maximum Likelihood tree for all the atypical D1 forms. See Figure 1. Of particular interests is the fact that they seem to follow an evolutionary pattern consistent with vertical descent and loss, although some likely events of later gene transfer can also be identified.

Figure 1. Updated tree of atypical D1 sequences.

Of particular interest is the appearance of numerous D1 fragments. Some of them are from incompletely sequenced genes, but some of them seem to be legitimate proteins, probably originating from partial gene duplication followed by divergence (Figure 2). A couple of these fragmented D1 seems to have phylogenetic affinity for the early evolving forms.

Figure 2. Sequence alignments of different D1. That marked with Fr. is the D1 fragment, found in the genome of some of the earliest evolving cyanobacteria strains, Synechococcus sp. PCC 7336. It seems to have some affinity for the G0 and early branching forms.