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Journal of Industrial Microbiology &... Apr 2022Alkanes are high-energy molecules that are compatible with enduring liquid fuel infrastructures, which make them highly suitable for being next-generation biofuels.... (Review)
Review
Alkanes are high-energy molecules that are compatible with enduring liquid fuel infrastructures, which make them highly suitable for being next-generation biofuels. Though biological production of alkanes has been reported in various microorganisms, the reports citing photosynthetic cyanobacteria as natural producers have been the most consistent for the long-chain alkanes and alkenes (C15-C19). However, the production of alkane in cyanobacteria is low, leading to its extraction being uneconomical for commercial purposes. In order to make alkane production economically feasible from cyanobacteria, the titre and yield need to be increased by several orders of magnitude. In the recent past, efforts have been made to enhance alkane production, although with a little gain in yield, leaving space for much improvement. Genetic manipulation in cyanobacteria is considered challenging, but recent advancements in genetic engineering tools may assist in manipulating the genome in order to enhance alkane production. Further, advancement in a basic understanding of metabolic pathways and gene functioning will guide future research for harvesting the potential of these tiny photosynthetically efficient factories. In this review, our focus would be to highlight the current knowledge available on cyanobacterial alkane production, and the potential aspects of developing cyanobacterium as an economical source of biofuel. Further insights into different metabolic pathways and hosts explored so far, and possible challenges in scaling up the production of alkanes will also be discussed.
Topics: Alkanes; Alkenes; Biofuels; Cyanobacteria; Metabolic Engineering
PubMed: 34718648
DOI: 10.1093/jimb/kuab075 -
Accounts of Chemical Research Dec 2023Every year, perhaps as much as 800 million tons of hydrocarbons enters the environment; alkanes make up a large percentage of it. Most are transformed by organisms that... (Review)
Review
Every year, perhaps as much as 800 million tons of hydrocarbons enters the environment; alkanes make up a large percentage of it. Most are transformed by organisms that utilize these molecules as sources of energy and carbon. Both aerobic and anaerobic alkane transformation chemistries exist, capitalizing on the presence of alkanes in both oxic and anoxic environments. Over the past 40 years, tremendous progress has been made in understanding the structure and mechanism of enzymes that catalyze the transformation of methane. By contrast, progress involving enzymes that transform liquid alkanes has been slower with the first structures of AlkB, the predominant aerobic alkane hydroxylase in the environment, appearing in 2023. Because of the fundamental importance of C-H bond activation chemistries, interest in understanding how biology activates and transforms alkanes is high.In this Account, we focus on steps we have taken to understand the mechanism and structure of alkane monooxygenase (AlkB), the metalloenzyme that dominates the transformation of liquid alkanes in the environment (not to be confused with another AlkB that is an α-ketogluturate-dependent enzyme involved in DNA repair). First, we briefly describe what is known about the prevalence of AlkB in the environment and its role in the carbon cycle. Then we review the key findings from our recent high-resolution cryoEM structure of AlkB and highlight important similarities and differences in the structures of members of class III diiron enzymes. Functional studies, which we summarize, from a number of single residue variants enable us to say a great deal about how the structure of AlkB facilitates its function. Next, we overview work from our laboratories using mechanistically diagnostic radical clock substrates to characterize the mechanism of AlkB and contextualize the results we have obtained on AlkB with results we have obtained on other alkane-oxidizing enzymes and explain these results in light of the enzyme's structure. Finally, we integrate recent work in our laboratories with information from prior studies of AlkB, and relevant model systems, to create a holistic picture of the enzyme. We end by pointing to critical questions that still need to be answered, questions about the electronic structure of the active site of the enzyme throughout the reaction cycle and about whether and to what extent the enzyme plays functional roles in biology beyond simply initiating the degradation of alkanes.
Topics: Cytochrome P-450 CYP4A; Alkanes; Hydrocarbons
PubMed: 38032826
DOI: 10.1021/acs.accounts.3c00590 -
Nature Microbiology Apr 2019Methanogenesis and anaerobic methane oxidation through methyl-coenzyme M reductase (MCR) as a key enzyme have been suggested to be basal pathways of archaea. How... (Review)
Review
Methanogenesis and anaerobic methane oxidation through methyl-coenzyme M reductase (MCR) as a key enzyme have been suggested to be basal pathways of archaea. How widespread MCR-based alkane metabolism is among archaea, where it occurs and how it evolved remain elusive. Here, we performed a global survey of MCR-encoding genomes based on metagenomic data from various environments. Eleven high-quality mcr-containing metagenomic-assembled genomes were obtained belonging to the Archaeoglobi in the Euryarchaeota, Hadesarchaeota and different TACK superphylum archaea, including the Nezhaarchaeota, Korarchaeota and Verstraetearchaeota. Archaeoglobi WYZ-LMO1 and WYZ-LMO3 and Korarchaeota WYZ-LMO9 encode both the (reverse) methanogenesis and the dissimilatory sulfate reduction pathway, suggesting that they have the genomic potential to couple both pathways in individual organisms. The Hadesarchaeota WYZ-LMO4-6 and Archaeoglobi JdFR-42 encode highly divergent MCRs, enzymes that may enable them to thrive on non-methane alkanes. The occurrence of mcr genes in different archaeal phyla indicates that MCR-based alkane metabolism is common in the domain of Archaea.
Topics: Alkanes; Archaea; Archaeal Proteins; Methane; Phylogeny
PubMed: 30833728
DOI: 10.1038/s41564-019-0364-2 -
World Journal of Microbiology &... Feb 2023Yarrowia lipolytica, a dimorphic yeast belonging to the Ascomycota, has potent abilities to utilize hydrophobic compounds, such as n-alkanes and fatty acids, as carbon... (Review)
Review
Yarrowia lipolytica, a dimorphic yeast belonging to the Ascomycota, has potent abilities to utilize hydrophobic compounds, such as n-alkanes and fatty acids, as carbon and energy sources. Yarrowia lipolytica can synthesize and accumulate large amounts of lipids, making it a promising host to produce various lipids and convert n-alkanes to useful compounds. For advanced use of Y. lipolytica in these applications, it is necessary to understand the metabolism of these hydrophobic compounds in this yeast and the underlying molecular mechanisms. In this review, current knowledge on the n-alkane metabolism and how this is regulated in Y. lipolytica is summarized. Furthermore, recent studies revealed that lipid transfer proteins are involved in the utilization of n-alkanes and the regulation of cell morphology in response to n-alkanes. This review discusses the roles of membrane lipids in these processes in Y. lipolytica.
Topics: Yarrowia; Alkanes; Fatty Acids
PubMed: 36781616
DOI: 10.1007/s11274-023-03541-3 -
Current Opinion in Chemical Biology Dec 2015Linear, branched and cyclic alkanes are important intermediates and end products of the chemical industry and are nowadays mainly obtained from fossil resources. In... (Review)
Review
Linear, branched and cyclic alkanes are important intermediates and end products of the chemical industry and are nowadays mainly obtained from fossil resources. In search for alternatives, biomass feedstocks are often presented as a renewable carbon source for the production of fuels, chemicals and materials. However, providing a complete market for all these applications seems unrealistic due to both financial and logistic issues. Despite the very large scale of current alkane-based fuel applications, biomass definitely has the potential to offer a partial solution to the fuel business. For the smaller market of chemicals and materials, a transition to biomass as main carbon source is more realistic and even probably unavoidable in the long term. The appropriate use and further development of integrated chemo- and biotechnological (catalytic) process strategies will be crucial to successfully accomplish this petro-to-bio feedstock transition. Furthermore, a selection of the most promising technologies from the available chemo- and biocatalytic tool box is presented. New opportunities will certainly arise when multidisciplinary approaches are further explored in the future. In an attempt to select the most appropriate biomass sources for each specific alkane-based application, a diagram inspired by van Krevelen is applied, taking into account both the C-number and the relative functionality of the product molecules.
Topics: Alkanes; Biocatalysis; Biomass; Biotechnology
PubMed: 26360875
DOI: 10.1016/j.cbpa.2015.08.010 -
The Journal of Physical Chemistry. A Dec 2014Ab initio computations, up to CCSD(T)/CBS on model systems, and MP2/cc-pVTZ and DFT calculations are performed on cation-alkane and cation-alkene complexes, cation =...
Ab initio computations, up to CCSD(T)/CBS on model systems, and MP2/cc-pVTZ and DFT calculations are performed on cation-alkane and cation-alkene complexes, cation = Li(+), Na(+), Be(2+), Mg(2+), Ca(2+), Cu(+) and Zn(2+); alkane = C(n)H2(n+2) (n = 1-10) and C6H12; and alkene = C2H4 and C6H6. Density functional theory-symmetry adapted perturbation theory (DFT-SAPT) calculations reveal that the cation-alkane interactions are predominantly constituted of induction component. The dramatic modulation of the strength of their interaction and the topological features obtained from atoms in molecules (AIM) analysis are consistent with the characteristics of a typical noncovalent interaction. In contrast to many of the conventional noncovalent interactions, cation-alkane interactions are substantially strong and are comparable in strength to the well studied cation-π interactions.
Topics: Alkanes; Cations; Metals; Quantum Theory
PubMed: 25384257
DOI: 10.1021/jp5076862 -
Journal of Biotechnology Mar 2016Alkanes constitute one of the vastest reserves of raw materials for the production of fine chemicals. This paper focuses on recent advances in alkane biohydroxylation,... (Review)
Review
Alkanes constitute one of the vastest reserves of raw materials for the production of fine chemicals. This paper focuses on recent advances in alkane biohydroxylation, i.e. the bioactivation of alkanes into their corresponding alcohols. Enzyme and whole-cell biocatalysts have been reviewed. Process considerations to implement such biocatalysts in bioreactors at large scale by coupling the bioconversion with cofactor regeneration and product removal are also discussed.
Topics: Alcohols; Alkanes; Biocatalysis; Bioreactors; Biotechnology; Hydroxylation
PubMed: 26853477
DOI: 10.1016/j.jbiotec.2016.02.007 -
Metallomics : Integrated Biometal... Aug 2011This review examines the metalloenzymes that catalyze the oxidation of alkanes in the environment. The focus of the review is on what is known about the relative... (Review)
Review
This review examines the metalloenzymes that catalyze the oxidation of alkanes in the environment. The focus of the review is on what is known about the relative abundances of these metalloenzymes, their metal ion requirements, and their reaction mechanisms. The relative significance of these reactions in the global transformation of alkanes is discussed.
Topics: Alkanes; Carbon Cycle; Environment; Enzymes; Metals; Oxidation-Reduction
PubMed: 21743926
DOI: 10.1039/c1mt00048a -
Biochemistry May 2022Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications.... (Review)
Review
Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications. Archaea are proposed to degrade short- and long-chain alkanes to CO by reversing methanogenesis, a theoretically reversible process. The pathway would start with alkane activation, an endergonic step catalyzed by methyl-coenzyme M reductase (MCR) homologues that would generate alkyl-thiols carried by coenzyme M. While the methane-generating MCR found in methanogens has been well characterized, the enzymatic activity of the putative alkane-fixing counterparts has not been validated so far. Such an absence of biochemical investigations contrasts with the current explosion of metagenomics data, which draws new potential alkane-oxidizing pathways in various archaeal phyla. Therefore, validating the physiological function of these putative alkane-fixing machines and investigating how their structures, catalytic mechanisms, and cofactors vary depending on the targeted alkane have become urgent needs. The first structural insights into the methane- and ethane-capturing MCRs highlighted unsuspected differences and proposed some explanations for their substrate specificity. This Perspective reviews the current physiological, biochemical, and structural knowledge of alkyl-CoM reductases and offers fresh ideas about the expected mechanistic and chemical differences among members of this broad family. We conclude with the challenges of the investigation of these particular enzymes, which might one day generate biofuels for our modern society.
Topics: Alkanes; Anaerobiosis; Archaea; Catalysis; Mesna; Methane; Oxidation-Reduction; Oxidoreductases; Phylogeny
PubMed: 35500274
DOI: 10.1021/acs.biochem.2c00135 -
Journal of Molecular Microbiology and... 2016The glycyl radical enzyme-catalyzed addition of n-alkanes to fumarate creates a C-C-bond between two concomitantly formed stereogenic carbon centers. The configurations... (Review)
Review
The glycyl radical enzyme-catalyzed addition of n-alkanes to fumarate creates a C-C-bond between two concomitantly formed stereogenic carbon centers. The configurations of the two diastereoisomers of the product resulting from n-hexane activation by the n-alkane-utilizing denitrifying bacterium strain HxN1, i.e. (1-methylpentyl)succinate, were assigned as (2S,1'R) and (2R,1'R). Experiments with stereospecifically deuterated n-(2,5-2H2)hexanes revealed that exclusively the pro-S hydrogen atom is abstracted from C2 of the n-alkane by the enzyme and later transferred back to C3 of the alkylsuccinate formed. These results indicate that the alkylsuccinate-forming reaction proceeds with an inversion of configuration at the carbon atom (C2) of the n-alkane forming the new C-C-bond, and thus stereochemically resembles a SN2-type reaction. Therefore, the reaction may occur in a concerted manner, which may avoid the highly energetic hex-2-yl radical as an intermediate. The reaction is associated with a significant primary kinetic isotope effect (kH/kD ≥3) for hydrogen, indicating that the homolytic C-H-bond cleavage is involved in the first irreversible step of the reaction mechanism. The (1-methylalkyl)succinate synthases of n-alkane-utilizing anaerobic bacteria apparently have very broad substrate ranges enabling them to activate not only aliphatic but also alkyl-aromatic hydrocarbons. Thus, two denitrifiers and one sulfate reducer were shown to convert the nongrowth substrate toluene to benzylsuccinate and further to the dead-end product benzoyl-CoA. For this purpose, however, the modified β-oxidation pathway known from alkylbenzene-utilizing bacteria was not employed, but rather the pathway used for n-alkane degradation involving CoA ligation, carbon skeleton rearrangement and decarboxylation. Furthermore, various n-alkane- and alkylbenzene-utilizing denitrifiers and sulfate reducers were found to be capable of forming benzyl alcohols from diverse alkylbenzenes, putatively via dehydrogenases. The thermophilic sulfate reducer strain TD3 forms n-alkylsuccinates during growth with n-alkanes or crude oil, which, based on the observed patterns of homologs, do not derive from a terminal activation of n-alkanes.
Topics: Acyl Coenzyme A; Alkanes; Anaerobiosis; Bacteria, Anaerobic; Biodegradation, Environmental; Metabolic Networks and Pathways; Oxidation-Reduction
PubMed: 26959725
DOI: 10.1159/000442160