<i>Promiscuous Anaerobes</i>

Grochowski, Laura L.; White, Robert H.

doi:10.1196/annals.1419.001

Cited by 11 publications

(4 citation statements)

References 152 publications

(265 reference statements)

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“…Different classes of FBP aldolases have been identified in archaea, bacteria, and eukaryotes (Say and Fuchs, 2010), and some FBP aldolases are also responsible for additional biological functions (Grochowski and White, 2008). All of the phototrophic bacteria, except FAPs, have the class II FBP aldolase (encoded by the fbaA gene), which has been mainly found in bacteria and fungi.…”

Section: Resultsmentioning

confidence: 99%

Carbon Metabolic Pathways in Phototrophic Bacteria and Their Broader Evolutionary Implications

Tang¹,

Tang²,

Blankenship³

2011

Front. Microbio.

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Photosynthesis is the biological process that converts solar energy to biomass, bio-products, and biofuel. It is the only major natural solar energy storage mechanism on Earth. To satisfy the increased demand for sustainable energy sources and identify the mechanism of photosynthetic carbon assimilation, which is one of the bottlenecks in photosynthesis, it is essential to understand the process of solar energy storage and associated carbon metabolism in photosynthetic organisms. Researchers have employed physiological studies, microbiological chemistry, enzyme assays, genome sequencing, transcriptomics, and 13C-based metabolomics/fluxomics to investigate central carbon metabolism and enzymes that operate in phototrophs. In this report, we review diverse CO2 assimilation pathways, acetate assimilation, carbohydrate catabolism, the tricarboxylic acid cycle and some key, and/or unconventional enzymes in central carbon metabolism of phototrophic microorganisms. We also discuss the reducing equivalent flow during photoautotrophic and photoheterotrophic growth, evolutionary links in the central carbon metabolic network, and correlations between photosynthetic and non-photosynthetic organisms. Considering the metabolic versatility in these fascinating and diverse photosynthetic bacteria, many essential questions in their central carbon metabolism still remain to be addressed.

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Section: Resultsmentioning

confidence: 99%

Carbon Metabolic Pathways in Phototrophic Bacteria and Their Broader Evolutionary Implications

Tang¹,

Tang²,

Blankenship³

2011

Front. Microbio.

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“…Many attributes of archaebacteria and eubacteria are so fundamentally different that, for lack of similar chemical intermediates in the pathway or for lack of subunit composition or sequence similarity, independent origin of the genes underlying those differences is the simplest explanation. Such differences include: (i) their membrane lipids (isoprene ethers versus fatty acid esters) [123], (ii) their cell walls (peptidoglycan versus S-layer) [124], (iii) their DNA maintenance machineries [116,125], (iv) the 31 ribosomal proteins that are present in archaebacteria but missing in eubacteria [126,127] (v) small nucleolar RNAs (homologues found in archaebacteria but not eubacteria) [128], (vi) archaebacterial versus eubacterial-type flagellae [129], (vii) their pathways for haem biosynthesis [130,131], (viii) eubacterial- versus archaebacterial-specific steps in the shikimate pathway [132,133], (ix) a eubacterial-type methylerythrol phosphate isoprene pathway versus an archaebacterial-type mevanolate isoprene pathway [134], (x) a eubacterial-type fructose-1,6-bisphosphate aldolase and bisphosphatase system versus the archaebacterial bifunctional aldolase-bisphosphatase [135], (xi) the typical eubacterial Embden–Meyerhoff (EM) and Entner–Doudoroff (ED) pathways of central carbohydrate metabolism versus the modified EM and ED pathways of archaebacteria [136], (xii) differences in cysteine biosynthesis [137], (xiii) different unrelated enzymes initiating riboflavin (and F 420 ) biosynthesis [138], and (xiv) in very good agreement with figure 2 b , different, unrelated, independently evolved enzymes in core pterin biosynthesis [139], to name a few examples. The pterin biosynthesis example is relevant because the cofactors H 4 F, H 4 MPT and MoCo, which are central to the eubacterial and archaebacterial manifestations of the Wood–Ljungdahl pathway are pterins (figure 2 d ), suggesting that methyl synthesis occurred geochemically (non-enzymatically) for a prolonged period of biochemical evolution.…”

Section: Rna and The Code Arose But That Is Not Our Focusmentioning

confidence: 99%

Early bioenergetic evolution

Sousa

Thiergart

Landan

et al. 2013

Phil. Trans. R. Soc. B

227

256

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Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. With regard to the possible temporal sequence of events, we focus on: (i) alkaline hydrothermal vents as the far-from-equilibrium setting, (ii) the Wood–Ljungdahl (acetyl-CoA) pathway as the route that could have underpinned carbon assimilation for these processes, (iii) biochemical divergence, within the naturally formed inorganic compartments at a hydrothermal mound, of geochemically confined replicating entities with a complexity below that of free-living prokaryotes, and (iv) acetogenesis and methanogenesis as the ancestral forms of carbon and energy metabolism in the first free-living ancestors of the eubacteria and archaebacteria, respectively. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent–ocean interface via the ATP synthase, (iii) harnessing of Na+ gradients generated by H+/Na+ antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. Of those five transitions, the first four are posited to have taken place at the vent. Ultimately, all of these bioenergetic processes depend, even today, upon CO2 reduction with low-potential ferredoxin (Fd), generated either chemosynthetically or photosynthetically, suggesting a reaction of the type ‘reduced iron → reduced carbon’ at the beginning of bioenergetic evolution.

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“…SAH is a product of SAM methyltransferases and is known to be a feedback inhibitor of these enzymes (16)(17)(18)(19). As a result of this inhibition, organisms have evolved efficient enzymes to metabolize SAH.…”

Section: Discussionmentioning

confidence: 99%

S-Inosyl-l-Homocysteine Hydrolase, a Novel Enzyme Involved inS-Adenosyl-l-Methionine Recycling

Miller

White

2015

J Bacteriol

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S-Adenosyl-L-homocysteine, the product of S-adenosyl-L-methionine (SAM) methyltransferases, is known to be a strong feedback inhibitor of these enzymes. A hydrolase specific for S-adenosyl-L-homocysteine produces L-homocysteine, which is remethylated to methionine and can be used to regenerate SAM. Here, we show that the annotated S-adenosyl-L-homocysteine hydrolase in Methanocaldococcus jannaschii is specific for the hydrolysis and synthesis of S-inosyl-L-homocysteine, not S-adenosyl-L-homocysteine. This is the first report of an enzyme specific for S-inosyl-L-homocysteine. As with S-adenosyl-L-homocysteine hydrolase, which shares greater than 45% sequence identity with the M. jannaschii homologue, the M. jannaschii enzyme was found to copurify with bound NAD ؉ and has K m values of 0.64 ؎ 0.4 mM, 0.0054 ؎ 0.006 mM, and 0.22 ؎ 0.11 mM for inosine, L-homocysteine, and S-inosyl-L-homocysteine, respectively. No enzymatic activity was detected with S-adenosyl-L-homocysteine as the substrate in either the synthesis or hydrolysis direction. These results prompted us to redesignate the M. jannaschii enzyme an S-inosyl-L-homocysteine hydrolase (SIHH). Identification of SIHH demonstrates a modified pathway in this methanogen for the regeneration of SAM from S-adenosyl-L-homocysteine that uses the deamination of S-adenosyl-L-homocysteine to form S-inosyl-L-homocysteine. IMPORTANCEIn strictly anaerobic methanogenic archaea, such as Methanocaldococcus jannaschii, canonical metabolic pathways are often not present, and instead, unique pathways that are deeply rooted on the phylogenetic tree are utilized by the organisms. Here, we discuss the recycling pathway for S-adenosyl-L-homocysteine, produced from S-adenosyl-L-methionine (SAM)-dependent methylation reactions, which uses a hydrolase specific for S-inosyl-L-homocysteine, an uncommon metabolite. Identification of the pathways and the enzymes involved in the unique pathways in the methanogens will provide insight into the biochemical reactions that were occurring when life originated. The recycling of S-adenosyl-L-methionine (SAM)-derived metabolites in Methanocaldococcus jannaschii was recently shown to use a novel enzyme, 5=-deoxyadenosine deaminase (DadD) (1). DadD deaminates three SAM-derived enzymatic products (5=-methylthioadenosine, 5=-deoxyadenosine, and S-adenosyl-L-homocysteine) to produce the inosine analogs ( Fig. 1) (1). The canonical pathway for recycling S-adenosyl-L-homocysteine (SAH) produced from SAM-dependent methyltransferases (2-4) proceeds in a three-step recycling pathway back to SAM (Fig. 2A). SAH is first hydrolyzed to produce adenosine and homocysteine using S-adenosyl-L-homocysteine hydrolase (SAHH). Homocysteine is then methylated by methionine synthase to produce methionine (5). The last step in the pathway is the generation of SAM by combining the adenosyl moiety of ATP with methionine to produce SAM, pyrophosphate, and phosphate (Fig. 2), catalyzed by SAM synthase (6). A similar pathway has been established in M. jannaschii but with ...

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Promiscuous Anaerobes

Cited by 11 publications

References 152 publications

Carbon Metabolic Pathways in Phototrophic Bacteria and Their Broader Evolutionary Implications

Carbon Metabolic Pathways in Phototrophic Bacteria and Their Broader Evolutionary Implications

Early bioenergetic evolution

S-Inosyl-l-Homocysteine Hydrolase, a Novel Enzyme Involved inS-Adenosyl-l-Methionine Recycling

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