Genomics of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia sp. Strain MED134

Abstract

Proteorhodopsin phototrophy is expected to have considerable impact on the ecology and biogeochemical roles of marine bacteria. However, the genetic features contributing to the success of proteorhodopsincontaining bacteria remain largely unknown. We investigated the genome of Dokdonia sp. strain MED134 (Bacteroidetes) for features potentially explaining its ability to grow better in light than darkness. MED134 has a relatively high number of peptidases, suggesting that amino acids are the main carbon and nitrogen sources. In addition, MED134 shares with other environmental genomes a reduction in gene copies at the expense of important ones, like membrane transporters, which might be compensated by the presence of the proteorhodopsin gene. The genome analyses suggest Dokdonia sp. MED134 is able to respond to light at least partly due to the presence of a strong flavobacterial consensus promoter sequence for the proteorhodopsin gene. Moreover, Dokdonia sp. MED134 has a complete set of anaplerotic enzymes likely to play a role in the adaptation of the carbon anabolism to the different sources of energy it can use, including light or various organic matter compounds. In addition to promoting growth, proteorhodopsin phototrophy could provide energy for the degradation of complex or recalcitrant organic matter, survival during periods of low nutrients, or uptake of amino acids and peptides at low concentrations. Our analysis suggests that the ability to harness light potentially makes MED134 less dependent on the amount and quality of organic matter or other nutrients. The genomic features reported here may well be among the keys to a successful photoheterotrophic lifestyle.

Ecology of marine Bacteroidetes: a comparative genomics approach

“…Comparison among four marine Bacteroidetes The basic properties of the four genomes analyzed in detail are shown in Table 1 Manually annotated genome published in González et al (2011). Genomics of marine Bacteroidetes B Fernández-Gómez et al Table 9).…”

“…The genome of another marine flavobacterium (Dokdonia sp. MED134; González et al, 2011) suggests that this PR-containing bacterium has similar characteristics to those of Polaribacter.…”

“…When looking at the distribution of these light sensing domains within PR þ bacteria, however, different patterns emerge (Supplementary Table 11 (González et al, 2011).…”

“…forsetii' KT0803 (Bauer et al, 2006) and Dokdonia sp. MED134 (González et al, 2011) genomes was manually curated and refined for each open reading frame, while the L. blandensis MED217 genome remains automatically annotated.…”

Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria

“…The objectives of the study were to evaluate: (i) whether the observed specific PR-driven responses to light are due to the presence or absence of specific functions within a particular bacterial genome, as recently hypothesized (González et al, 2011;Riedel et al, 2013) and (ii) whether the energy generated by PR could be used for the uptake of exogenic organic molecules (for example, B-vitamins). To accomplish this, we compared three bacteria in the genus Dokdonia (MED134 from the Mediterranean Sea, PRO95 from the North Sea, and DSW-1 T from the East Sea of Korea), which contain PR genes and respond differently to light exposure.…”