Hydrogen Formation and Its Regulation in Ruminococcus albus: Involvement of an Electron-Bifurcating [FeFe]-Hydrogenase, of a Non-Electron-Bifurcating [FeFe]-Hydrogenase, and of a Putative Hydrogen-Sensing [FeFe]-Hydrogenase

Abstract

bRuminococcus albus 7 has played a key role in the development of the concept of interspecies hydrogen transfer. The rumen bacterium ferments glucose to 1.3 acetate, 0.7 ethanol, 2 CO 2 , and 2.6 H 2 when growing in batch culture and to 2 acetate, 2 CO 2 , and 4 H 2 when growing in continuous culture in syntrophic association with H 2 -consuming microorganisms that keep the H 2 partial pressure low. The organism uses NAD ؉ and ferredoxin for glucose oxidation to acetyl coenzyme A (acetyl-CoA) and CO 2 , NADH for the reduction of acetyl-CoA to ethanol, and NADH and reduced ferredoxin for the reduction of protons to H 2 . Of all the enzymes involved, only the enzyme catalyzing the formation of H 2 from NADH remained unknown. Here, we report that R. T he genus Ruminococcus (class Clostridia) consists of species of anaerobic, Gram-positive bacteria. One or more species of this genus are found in significant numbers in the intestines of humans (enterotype 3) (1, 2) and in the rumen and colon of herbivores (3, 4). Ruminococcus flavefaciens and Ruminococcus albus are among the most important plant cell wall-degrading bacteria in the rumen. These two species produce all required enzymes for hydrolyzing the plant cell wall polysaccharides, cellulose and hemicellulose (5, 6).R. albus was isolated in 1957 from the rumen of cattle by Hungate (7,8), who showed that in batch culture the bacterium ferments cellulose, cellobiose, or glucose to acetate, CO 2 , ethanol, and H 2 . Nevertheless, neither H 2 nor ethanol accumulate to high concentrations in the rumen (9, 10). The low H 2 concentrations in the rumen have been explained by the presence of H 2 -consuming microorganisms, such as Methanobrevibacter ruminantium (formerly Methanobacterium ruminantium), that consume H 2 more rapidly than it is formed from cellulose by R. albus (11). The laboratory of Bryant and Wolin then showed in 1973 that the fermentation of glucose by R. albus strain 7 was shifted from 1.3 acetic acid, 0.7 ethanol, 2 CO 2 , and 2.6 H 2 in batch culture to 2 acetic acid, 2 CO 2 , and 4 H 2 in chemostat culture together with Wolinella succinogenes (formerly Vibrio succinogenes), which grew on H 2 and fumarate producing succinate, keeping the H 2 concentration low (12). The interspecies cooperation allowed W. succinogenes to grow at the expense of H 2 produced by R. albus, but it also offered an energetic advantage to R. albus in the form of a higher ATP gain (4 mol of ATP instead of 3.3 mol of glucose fermented) and, consequently, a better growth yield (13). At low H 2 partial pressures, the free energy associated with glucose fermentation is more negative than that at high H 2 partial pressures, which is the thermodynamic basis for the different ATP gains (13). The fermentation of R. albus on glucose has been modeled (14). The literature on interspecies H 2 and formate transfer has been reviewed recently (15).Enzymatic analyses have revealed that R. albus strain 7 grown in batch culture on glucose contains an NAD-specific glyceraldehyde-3-phosphate dehydr...

The Bifunctional Alcohol and Aldehyde Dehydrogenase Gene, adhE , Is Necessary for Ethanol Production in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum

“…1C). A similar organization recently was identified in a study of Ruminococcus albus hydrogenases, where rex, Ra_adhE, and hydS were in a transcriptional unit with a putative ferredoxindependent hydrogenase, and this locus is believed to play an important part in the sensory and regulatory mechanism of electron metabolism in R. albus (44). In C. thermocellum, this gene cluster may play a similar role.…”

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

“…As with the group 2b and 2c [NiFe]-hydrogenases, the operons encoding these hydrogenases contain predicted PAS domains (Figure 2) that likely transduce the signal of hydrogenase activity to downstream components via a redox-active heme. There is some transcriptional evidence that the putative phosphatase-linked sensory hydrogenases of Thermoanaerobacterium saccharolyticum (Shaw et al, 2009) and Ruminococcus albus (Zheng et al, 2014) regulate the transcription of group A [FeFe]-hydrogenases, but it has yet to be biochemically confirmed that these enzymes have a regulatory role. Other sensory hydrogenases may regulate wider cellular functions (for example, motility) in response to changes of pH 2 in anoxic environments.…”

“…In parallel, the discovery of electron bifurcation has expanded our understanding of how energy is conserved in anaerobic processes such as cellulolytic fermentation, acetogenesis and methanogenesis (Schut and Adams, 2009;Kaster et al, 2011;Buckel and Thauer, 2013;Schuchmann and Muller, 2014). Other themes, including H 2 sensing within anaerobes (Zheng et al, 2014) and H 2 fermentation in aerobes , are emerging.…”

H2metabolism is widespread and diverse among human colonic microbes

“…26 There is also growing evidence that H 2 sensing has a role in anaerobic microorganisms. 19,29 This assortment of functions is supported by the great phylogenetic diversity of the hydrogenases. 19 Hydrogenases can be subdivided into 3 distinct classes based on their metal site, the [NiFe], 20 [FeFe], 23 and [FeFe] hydrogenases are highly diverse in their redox centers, associated subunits, and wider cellular integration.…”