Enzymes and genes involved in aerobic alkane degradation

1Various microorganisms, including bacteria, filamentous fungi and yeasts, can degrade alkanes. Notably, some recently characterized bacterial species are highly specialized for hydrocarbon degradation. These species are called hydrocarbonoclastic bacteria (HCB), and they play a key role in the removal of hydrocarbons from polluted and non-polluted environments.

2Of particular importance is Alcanivorax, a marine bacterium that can assimilate various linear or branched alkanes but that is unable to metabolize aromatic hydrocarbons, sugars, amino acids, and most other common carbon sources. Alcanivorax bacteria are present in non-polluted seawater in low numbers; however, the number of Alcanivorax can increase as a result of an oil spill, and they are believed to play an important role in the natural bioremediation of oil spills worldwide.

3More recently, other HCBs belonging to the genera Thalassolituus, Oleiphilus, Oleispira, Marinobacter, Bacillus and Geobacillus have also been shown to play an important role in the degradation of oil spills in marine environments.

4Several reviews have covered different aspects of the physiology, enzymes and pathways that are responsible for alkane degradation. This review focuses on recent advances in alkane chemotaxis, across membrane transport and gene regulations. In addition, newly discovered enzymes that are responsible for long-chain alkane mineralization are also discussed.

5Chemotaxis facilitates the movement of microorganisms toward or away from chemical gradients in the environment, and this process plays a role in biodegradation by bringing cells into contact with degradation substrates. Alkanes are sources of carbon and energy for many bacterial species and have been shown to function as chemo-attractants for certain microorganisms. A bacterial Flavimonas oryzihabitans isolate that was obtained from soil contaminated with gas oil was shown to be chemotactic to gas oil and hexadecane. Similarly, Pseudomonas aeruginosa PAO1 is chemotactic to hexadecane. The tlpS gene, which is located downstream of the alkane hydroxylase gene alkB1 in the PAO1 genome, is predicted to encode membrane-bound methyl-accepting chemotaxis proteins (MCP) that may play a role in alkane chemotaxis, although no experimental evidence exists. Similarly, the gene alkN is predicted to encode an MCP that could be involved in alkane chemotaxis in P. putida GPo1. Our recent investigation of the genome sequence of Alcanivorax dieselolei B-5 identified the alkane chemotaxis machinery of Alcanivorax, which consists of eight cytoplasmic chemotaxis proteins that transmit signals from the MCP proteins to the flagellar motors (Figure 1). This chemotaxis machinery is similar to that of Escherichia coli. However, further investigation is necessary to confirm the mechanism of alkane chemotaxis in A. dieselolei B-5.

6Although the genes and proteins that enable the passage of aromatic hydrocarbons across the bacterial outer membrane have been identified, the active transport mechanisms involved in alkane uptake remain unclear. Previous reviews discussed the observation that direct uptake of alkane molecules from the water phase is only possible for low molecular weight alkanes, which are sufficiently soluble to facilitate efficient transport into cells. For medium- and long-chain n-alkanes, microorganisms may gain access to these compounds by adhering to hydrocarbon droplets (which is facilitated by the hydrophobic cell surface) or by surfactant-facilitated access, as reviewed by. Surfactants have been reported to increase the uptake and assimilation of alkanes, such as hexadecane, in liquid culture, but their exact role in alkane uptake is not fully understood. Bacteria that are capable of oil degradation usually produce and secrete surfactants of diverse chemical nature that allow alkane emulsification. Based on our understanding of biosurfactant structure and the mechanism of outer membrane transport, we speculate that biosurfactants may be excluded from entering the cell and remain in the extracellular milieu.

7In P. putida, alkL in the alk operon is postulated to play an important role in alkane transport into the cell. Transcriptome analysis of A. borkumensis Sk2 revealed that the alkane-induced gene blc, encoding the outer membrane lipoprotein Blc, might be involved in alkane uptake because it contains a so-called lipocalin domain. When this domain contacts organic solvents, a small hydrophobic pocket forms and catalyzes the transport of small hydrophobic molecules. More recently, our genome analysis and closer examination of A. dieselolei B-5indicated that three outer membrane proteins that belong to the long-chain fatty acid transporter protein (FadL) family are involved in alkane transport (unpublished). The FadL homologs are present in many bacteria that are involved in the biodegradation of xenobiotics, which are usually hydrophobic and probably enter cells by a mechanism similar to that employed for long-chain (LC) fatty acids by FadL in E. coli.

8The initial terminal hydroxylation of n-alkanes can be carried out by enzymes that belong to different families. Microorganisms degrading short-chain length alkanes (C2–C4, where the subindex indicates the number of carbon atoms of the alkane molecule) have enzymes related to methane monooxygenases. Strains degrading medium-chain length alkanes (C5–C17) frequently contain soluble cytochrome P450s and integral membrane non-heme iron monooxygenases, such as AlkB.

9Interestingly, alkane hydroxylases of long-chain length (LC-) alkanes (>C18) are unrelated to the above alkane hydroxylases as characterized recently. One such hydroxylase, AlmA, is an LC-alkane monooxygenase from Acinetobacter. A second hydroxylase is LadA, which is a thermophilic soluble LC-alkane monooxygenase from Geobacillus.

10The almA gene, which encodes a putative monooxygenase belonging to the flavin-binding family, was identified from Acinetobacter sp. DSM 17874. This gene encodes the first experimentally confirmed enzyme that is involved in the metabolism of LC n-alkanes of C32 and longer. We provided the first evidence that the AlmA of the genus Alcanivorax functions as an LC-alkane hydroxylase, and found that the gene almA in both A. hongdengensis A-11-3 and A. dieselolei B-5 strains expressed at high levels to facilitate the efficient degradation of LC n-alkanes. The almA gene sequences were present in several bacterial genera capable of LC n-alkane degradation, including Alcanivorax, Marinobacter, Acinetobacter, and Parvibaculum. In addition, similar genes are found in other genera in GenBank, such as Oceanobacter sp. RED65, Ralstonia spp., Mycobacterium spp., Photorhabdus sp., Psychrobacter spp., and Nocardia farcinica IFM10152. However, few of these genes have been functionally characterized.

11A unique LC-alkane hydroxylase from the thermophilic bacterium Geobacillus thermodenitrificans NG80-2 has been characterized. This enzyme is called LadA and oxidizes C15–C36 alkanes, generating the corresponding primary alcohols. The LadA crystal structure has been identified, revealing that LadA belongs to the bacterial luciferase family, which is two-component, flavin-dependent oxygenase. LadA is believed to oxidize alkanes by a mechanism similar to that of other flavoprotein monooxygenases, and its ability to recognize and hydroxylate LC-alkanes most likely results from the way in which it captures the alkane. Therefore, the hydroxylases involved in LC-alkane degradation appear to have evolved specifically, which is in contrast with other alkane monooxygenases such as AlkB and P450.

12Interestingly, branched-chain alkanes are thought to be more difficult to degrade than linear alkanes. However, Alcanivorax bacteria efficiently degrade branched alkanes. In A. borkumensis SK2, isoprenoid hydrocarbon (phytane) strongly induces P450 (a) and alkB2. In a previous report, we found that both pristane and phytane activate the expression of alkB1 and almA in A. dieselolei B-5. In A. hongdengensis A-11-3, we recently found that pristane selectively activates the expression of alkB1, P450-3 and almA. However, the metabolic pathways that mediate this activity are poorly understood, although they may involve the ω- or β-oxidation of the hydrocarbon molecule.

13The expression of the bacterial genes involved in alkane assimilation is tightly regulated. Alkane-responsive regulators ensure that alkane degradation genes are induced only in the presence of the appropriate hydrocarbons. Many microorganisms contain several sets of alkane degradation systems, each one being active on a particular kind of alkane or being expressed under specific physiological conditions. In these cases, the regulatory mechanisms should assure an appropriate differential expression of each set of enzymes. The regulators that have been characterized belong to different families, including LuxR/MalT, AraC/XylS, and other non-related families (Table 1).

14Pseudomonas butanovora species oxidize C2–C8 n-alkanes into the corresponding alcohols with an alkane monooxygenase termed butane monooxygenase (BMO). BMO is a multimeric protein that is formed by the products of the bmoXYBZDC operon. The expression of the genes encoding BMO is activated by BmoR, a δ54-dependent transcriptional regulator that recognizes alcohols and aldehydes derived from the C2–C8 n-alkanes that are substrates of BMO, although BmoR does not recognize the alkanes themselves.

15In P. putida GPo1, the OCT plasmid encodes all of the genes required for the assimilation of C3–C13 alkanes. The genes in this pathway are grouped into two clusters, alkBFGHJKL and alkST. The alkBFGHJKL operon is transcribed from a promoter named PalkB, whose expression requires the transcriptional activator AlkS and the presence of alkanes. An AlkS-dependent reporter system based on a PalkB-luxAB fusion showed that C5–C10 alkanes are efficient activators of the AlkS regulator. When alkanes become available, AlkS binds and represses PalkS1 more efficiently than it does in the absence of alkanes. From this binding site, AlkS activates the PalkS2 promoter, resulting in high expression of the alkST genes. Therefore, this pathway is controlled by a positive feedback mechanism that is driven by AlkS.

16A gene similar to alkS in P. putida GPo1 is located upstream of alkB1 in A. borkumensis SK2, and AlkS is predicted to be an alkane-responsive transcriptional activator. The expression level of AlkS in strain SK2 cells grown in hexadecane is higher than that of pyruvate-grown cells. Evidence suggests that in A. borkumensis, AlkS activates the expression of alkB1, a gene that encodes an alkane hydroxylase, in response to alkanes. However, it is unlikely that AlkS regulates the expression of alkB2, despite the induction of this gene in response to alkanes. Interestingly, a gene encoding a transcriptional regulator belonging to the GntR family is located immediately upstream of alkB2; however, its role in alkB2 expression has not been reported. A. borkumensis has three genes encoding cytochrome P450 of the CYP153 family. A gene encoding a transcriptional regulator belonging to the AraC family is located close to P450-1, but its role in regulating the P450-1 gene cluster has not been investigated.

17In A. hongdengensis, a gene downstream of alkB1 encodes a protein that is similar to TetR family transcriptional regulators. In addition, a gene encoding a transcriptional regulator belonging to the GntR family is located just upstream of alkB2, although its role in the regulation of alkB2 is not known. Genes encoding transcriptional regulators belonging to the AraC family are located near P450-1 and P450-2. Similar to many of the genes described above, their role in the regulation of the corresponding P450 genes requires further investigation.

18Three regulators that are involved in alkane degradation were identified in the A. dieselolei strain B-5 genome sequence, and they belong to different MerR and AraC families (Table 1). Regulatory genes are located upstream of alkB1 and P450, and the proteins encoded by these genes are 46 and 64% similar to MerR and AraC from P. aeruginosa and A. borkumensis SK2, respectively. Downstream of alkB2, there is a gene encoding a transcriptional regulator that shares 61% similarity with AraC from Marinobacter sp. ELB17. Therefore, Alcanivorax strains usually encode multiple alkane hydroxylases that are expressed under the control of different regulators encoded in the same gene cluster as the monooxygenase gene. Our lab is using strain B-5 as a model system to study how cells modulate the expression of these genes in response to different alkanes with varied chain lengths.

19The expression of alkane degradation pathway genes is often down regulated by complex global regulatory controls that ensure that the genes are expressed only under the appropriate physiological conditions or in the absence of any preferred compounds. Two global regulatory networks exist. One network relies on the global regulatory protein Crc, while the other network receives information from cytochrome o ubiquinol oxidase (Cyo), which is a component of the electron transport chain.

20The Crc is an RNA-binding protein that interacts with the 5′ end of the alkS mRNA, inhibiting translation. A recent study further showed that Crc inhibits the induction of the alkane degradation pathway by limiting not only the translation of their transcriptional activators but also that of genes involved in the entire alkane degradation pathway in P. putida. In addition, results of this study suggests that Crc follows a multi-step strategy in many cases, targeting uptake, transcription regulation, and/or the production of the associated pathways’ catabolic enzymes.

21However, when cells grow in a minimal salt medium containing succinate as the carbon source, the activity of Crc is low; instead, Cyo terminal oxidase play a key role in the global control that inhibits the induction of the alkane degradation genes. Cyo is one of the five terminal oxidases that have been characterized in P. putida. Inactivation of the Cyo terminal oxidase partially relieves the repression exerted on the alkane degradation pathway under several conditions, while inactivation of any of the other four terminal oxidases does not. Cyo affects the expression of many other genes, and this enzyme has been proposed to be a component of a global regulatory network that transmits information regarding the activity of the electron transport chain to coordinate respiration and carbon metabolism. The expression of the cyo genes encoding the subunits of Cyo terminal oxidase varies depending on oxygen levels and carbon source, and there is a clear correlation between Cyo levels and the extent of alkane degradation pathway repression.

22Research in the last few years has resulted in many new insights into the mechanism of alkane degradation by microorganisms, including the upstream regulations and the long-chain length alkane oxidation. Investigations using “omics” strategies will help us to better understand the global metabolic networks within a microbial cell and the overall process of bacterial alkane-dependent chemotaxis, alkane transport, gene expression regulation and complete mineralization.

23The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.