Methanococcus maripaludis

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Methanococcus maripaludis
Electron micrograph of Methanococcus maripaludis.png
Electron micrograph showing prominent archaeal features and interior body of the microorganism. Courtesy of Dr. Ken F. Jarrell and Shin-Ichi Aizawa. Mag bar of 500nm.
Scientific classification
Domain:
Archaea
Kingdom:
Euryarchaeota
Phylum:
Euryarchaeota
Class:
Methanococci
Order:
Methanococcales
Family:
Methanococcaceae
Genus:
Methanococcus
Species:
Methanococcus maripaludis

Jones et al. 1984

Methanococcus maripaludis is a species of methanogenic archaea found in marine environments, predominantly salt marshes. [1] M. maripaludis is a non-pathogenic, gram-negative, weakly motile, non-spore-forming, and strictly anaerobic mesophile. [2] It is classified as a chemolithoautotroph. [3] This archaeon has a pleomorphic coccoid-rod shape of 1.2 by 1.6 μm, in average size, and has many unique metabolic processes that aid in survival. [2] [4] M. maripaludis also has a sequenced genome consisting of around 1.7 Mbp with over 1,700 identified protein-coding genes. [5] In ideal conditions, M. maripaludis grows quickly and can double every two hours. [4]

Contents

Metabolism

The metabolic landscape of M. maripaludis consists of eight major subsystems which provide pathways for energy generation and cell growth. These subsystems include amino acid metabolism, glycolysis/glycogen metabolism, methanogenesis, nitrogen metabolism, non-oxidative pentose phosphate pathway (NOPPP), nucleotide metabolism, and the reductive citric acid (RTCA) cycle. [4]

Methanogenesis, the process of reducing carbon dioxide to methane, serves as the primary pathway for energy generation using coenzymes and a membrane-bound enzyme complex. [6] The methanogenesis pathway uses the same carbon source as the remaining seven subsystems for cell growth. [4] Additionally, the subsystems use two essential intermediates, acetyl CoA and pyruvate, to produce precursors critical for cell growth. [4]

Amino acid

M. maripaludis uses carbon dioxide and acetate as substrates for amino acid biosynthesis. [4] Each of these substrates can produce Acetyl-CoA through various mechanisms. [4] Using carbon dioxide, M. maripaludis can generate Acetyl-CoA from methyl-THMPT, an intermediate of methanogenesis, and carbon monoxide, produced from the reduction of carbon dioxide. [4] Using acetate, Acetyl-CoA is synthesized from the AMP-forming acetate CoA ligase. [4] Acetyl-CoA then acts as a precursor to pyruvate, which promotes methanogenesis and alanine biosynthesis. [4] Pyruvate can be converted to L-alanine via alanine dehydrogenase, which is a reversible reaction. Once alanine is synthesized, it can be transported into the microbe via alanine permease. [4]

Glycolysis with formation of glycogen

M. maripaludis has a modified Embden Meyerhof-Parnas (EMP) pathway, a glycolysis pathway. Dissimilarly to other organisms that reduce NAD to NADH in the EMP Pathway, M. maripaludis reduces ferrodoxins. Additionally, the protein kinases, responsible for transferring phosphate groups between compounds, uniquely rely on ADP rather than ATP. [4] Additionally, M. maripaludis is also capable of synthesizing glycogen. [4] Due to experimentally observed activities of enzymes involved in both the catabolic and anabolic directions of the EMP Pathway, the latter is utilized to a higher extent, resulting in the formation of glycogen stores. [4]

Methanogenesis

In M. maripaludis, the primary carbon source for methanogenesis is carbon dioxide, although alternatives such as formate are also used. Though all methanogens use certain key coenzymes, cofactors, and intermediates to produce methane, M. maripaludis undergoes the Wolfe cycle, which converts CO2 and hydrogen gas into methane and H2O. [7] 7 different hydrogenases are present in M. maripaludis that allow for the usage of H2 as an electron donor to reduce CO2. [4] Some strains and mutants of M. maripaludis have been shown to be capable of methanogenesis in the absence of hydrogen gas, though this is uncommon. [8]

Methanogenesis in M. maripaludis occurs in the following steps:

  1. Reduction of CO2 via methanofuran and reduced ferredoxins [9]
  2. Oxidation and subsequent reduction of the coenzyme F420 in the presence of H2 [10] [9]
  3. Transfer of a methyl group from methyl-THMPT to coenzyme M (HS-CoM), driving translocation of 2 Na+ across the membrane to strengthen the proton gradient [11]
  4. Demethylation of methyl-S-CoM to form methane and generate additional energy via the subsequent reduction of byproducts with H2 [12]

Nitrogen

M. maripaludis uses three sources of nitrogen: ammonia, alanine, and dinitrogen with ammonia. [4] Nitrogen assimilation occurs in the bacteria through ammonia when an inorganic nitrogen compound is converted to an organic nitrogen compound. In M. maripaludis, glutamine synthetase is used to make glutamine from glutamate and ammonia. The glutamine created then is sent to continue through protein synthesis. [4]

M. maripaludis uses alanine racemase and alanine permease for alanine uptake. [4] A racemase enzyme is used to convert the inversion of stereochemistry within the molecule while a permease is a protein that catalyzes the transport of a molecule across the membrane. [13]

Free N2 fixation is well established in M. maripaludis. M. maripaludis contains a multiprotein nitrogen complex containing an Fe protein and a MoFe. [4] The ferredoxin is reduced and reduces the oxidized Fe, stripping the Fe of its electrons in the presence of N2. The now reduced Fe protein is oxidized by ATP, reducing the MoFe protein. [4] The MoFe protein then reduces N2 to ammonia. This reductive step uses the electrons from the reduced ferredoxin which requires high amounts of energy. N2 fixation is unfavorable in M. maripaludis because of the high energy demand, so it is common for a cell to not activate this fixation pathway when ammonia and alanine are available. [4]

Pentose phosphate pathway

The pentose phosphate pathway is essential for M. maripaludis to make nucleotides and nucleic acids. [4] M. maripaludis contains high activities of non-oxidative enzymes, but has no oxidative enzyme activities. [4] Non-oxidative means that the enzymes do not have the ability to combine with oxygen and oxidize. The non-oxidative pentose phosphate pathway (NOPPP) is regulated and used through substrate availability. In M. maripaludis, ribulose-5-phosphate is converted to erythrose-4-phosphate and fructose-6-phosphate. [4] Four enzymes are used in this conversion: transketoloase, ribulose-phosphate 3-epimerase, ribose-5-phosphate isomerase, and translaldolase. [4]

Nucleotide metabolism

Nucleotide metabolism by M. maripaludis is well understood. For nucleic acid biosynthesis, the methanogen must produce pyrimidines, such as uridine triphosphate (UTP) and cytidine triphosphate (CTP), as well as purines such as guanine triphosphate (GTP) and adenosine triphosphate (ATP). To synthesize the pyrimidines, phosphoribosyl pyrophosphate (PRPP) combines with bicarbonate, L-glutamine, or orotate. This combination synthesizes uridine monophosphate, which can then be converted into uridine triphosphate (UTP). UMP also functions as a precursor to CTP. [4] To synthesize the purines, inosinic acid (IMP) is first made via a series of reactions, which include PRPP combining with glutamine to form 5-phosphoribosylamine. This reaction is catalyzed by PRPP synthetase. Once IMP is synthesized, it can be further converted into adenosine monophosphate (AMP) and guanine monophosphate (GMP). To synthesize AMP, IMP combines with adenylosuccinate. To synthesize GMP, IMP is converted into xanthine monophosphate (XMP) which can then be converted into GMP. [4]

Reductive Citric Acid (RTCA) Cycle

The tricarboxylic acid cycle serves as a central metabolic pathway in aerobic organisms. It plays an essential role in energy production and biosynthesis by generating electron carriers such as NADH and FAD. [14] This is performed by oxidizing acetyl-CoA, derived from various nutrients and complex carbon molecules, to CO2 and H2O. [4]

M. maripaludis, a strictly anaerobic mesophile, undergoes an incomplete Reductive Citric Acid (RTA) Cycle to reduce CO2 and H2O and synthesize complex carbon molecules. [4] Lacking several steps and essential enzymes, including phosphoenolpyruvate carboxykinase, citrate synthase, aconitate, and isocitrate dehydrogenase, hinders the completion of this cycle. [15] [4] Pyruvate, produced from glycolysis/gluconeogenesis, is an initial metabolite in M. maripaludis for the Tricarboxylic Acid Cycle.

Cell structure

The irregular-shaped, weakly-motile coccus, Methanococcus maripaludis, has a diameter of 0.9-1.3 μm with a single, electron-dense S-layer lacking peptidoglycan. These characteristics assist in identifying its domain as Archaea. [4] Commonly found in methanogens, their cell walls lack murein and ether-linked membrane lipids, among other biochemical properties. [16] The S-layer is composed of glycoproteins that enclose the entire cell and help to protect the cell from direct interactions with the environment. More specifically, the S-layer provides archaeal cells a stabilization barrier that is resistant to environmental changes. [17] Additionally, M. maripaludis consists of two surface appendages assisting in motility: flagella and pili. [4]

Flagella and pili

Electron micrograph illustrating both flagellated, Mm900, and non-flagellated cells, DFlaG, of Methanococcus maripaludis. Electron micrographs depicting both flagellated and non-flagellated Methanococcus maripaludis cells.png
Electron micrograph illustrating both flagellated, Mm900, and non-flagellated cells, ΔFlaG, of Methanococcus maripaludis.

Archaeal flagella contain distinctive prokaryotic motility structures that are similar to bacterial type IV pili (T4P). They are constructed from proteins bearing class III signal peptides that are cleaved by specific signal peptidases. They also possess homologous genes, which encode an ATPase, and conserved membrane proteins for appendage assembly. [17] The flagellum of M. maripaludis is composed of three flagellin glycoproteins, which are all modified with an N-linked tetrasaccharide. This is critical for continued attachment to surfaces, cell-to-cell contact, and locomotion. [17] Both flagella and pili structures are used to attach to surfaces, allowing them the ability to remain in desirable environments. [17]

M. maripaludis encompasses a complete set of fla genes with three distinct flagellin genes, flaB1, flaB2 and flaB3, and the remaining eight genes including flaC-flaJ. [18] From the flagella locus, there are two major flagellin proteins required for flagella filaments, flaB1 and flaB2. Flagellin export also requires two specific proteins including flaH and flaI. The hook-like protein in M. maripaludis is strongly indicated by the minor flagellin protein, flaB3. [18] The flagella in numerous archaea undergo post-translational modifications, including glycosylation. Consequently, these flagella exhibit larger proteins than their expected gene sequence. [18]

Similar to the flagella, the proteins involved in the pilus assembly of M. maripaludis exhibit resemblance to bacterial Type IV pili due to the presence of an N-terminal signal peptide and an anticipated N-terminal hydrophobic α-helix. [19] [20] The two pilin-like genes, MMP0236 (epdB) and MMP0237 (epdC), possess a short, atypical signal peptide ending in a conserved glycine. This is then succeeded by a hydrophobic segment, resulting in a distinct quaternary structure and pilus formation. [20]

Genetics

Methanococcus maripaludis is one of four hydrogenotrophic methanogens, along with Methanocaldococcus jannaschii, Methanothermobacter thermautotrophicus, and Methanopyrus kandleri , to have its genome sequenced. [4] Of these three, Methanocaldococcus jannaschii is the closest living, known relative of M. maripaludis.M. maripaludis, like many other archaea, has one single circular chromosome. [4] According to the number of BlastP hits in the genome sequence, or similar protein sequences identified by the Basic Local Alignment Search Tool (BLAST), M. maripaludis is similar to most other methanogens. [4] However, M. maripaludis is missing common features, such as the ribulose bisphosphate carboxylase enzyme. [4]

Twenty one different strains of M. maripaludis have had their genomes sequenced, and each genome includes many copies of the chromosome in the singular cell, ranging from 5 to 55. [21] Of its 1,722 protein coding genes, 835 ORFs, or open reading frames, have unknown functions, and 129 ORFs are unique to M. maripaludis. [4] Some of these genes have been identified using in vivo transposon mutagenesis that may be essential for growth, making up approximately 30% of the genome. [22] The sequenced genome also revealed about 48 protein transporter systems, largely dominated by ABC transporters followed by iron transporters. [5]

M. maripaludis has been genetically altered to produce non-native, desired products, such as geraniol and polyhydroxybutyrate. [21] M. maripaludis can be used to sequence a variety of promoters and ribosome-binding sites using CRISPR/Cas9 technology. [23] Large deletions in the DNA can also be facilitated by a CRISPR/Cas9 system specifically designed for a strain named S0001. [21]

Environmental roles

Methanogens play important roles in waste water treatment, carbon conversion, hydrogen production, and many other environmental processes. [4] In terms of waste water treatment, methanogens have been used to anaerobically degrade waste into methane utilizing a symbiotic relationship with syntrophic bacteria. [4] M. maripaludis, in addition to other methanogens, has the potential for generating fuels, such as methane and methanol, from CO2 emissions due to native CO2 uptake. [4] CO2 emissions are currently one of the leading sources of global warming. The ability of M. maripaludis to uptake CO2 from the environment in the presence of N2 allows for a potential route for conversion of CO2 emissions to a useful fuel like methane. [4] It is able to capture and convert CO2 from power and chemical plant emissions as well. Despite the many potential applications, the need for large amounts of hydrogen is an issue with using any methanogen for biomethane production. [4]

Related Research Articles

Methanogens are anaerobic archaea that produce methane as a byproduct of their energy metabolism, i.e., catabolism. Methane production, or methanogenesis, is the only biochemical pathway for ATP generation in methanogens. All known methanogens belong exclusively to the domain Archaea, although some bacteria, plants, and animal cells are also known to produce methane. However, the biochemical pathway for methane production in these organisms differs from that in methanogens and does not contribute to ATP formation. Methanogens belong to various phyla within the domain Archaea. Previous studies placed all known methanogens into the superphylum Euryarchaeota. However, recent phylogenomic data have led to their reclassification into several different phyla. Methanogens are common in various anoxic environments, such as marine and freshwater sediments, wetlands, the digestive tracts of animals, wastewater treatment plants, rice paddy soil, and landfills. While some methanogens are extremophiles, such as Methanopyrus kandleri, which grows between 84 and 110°C, or Methanonatronarchaeum thermophilum, which grows at a pH range of 8.2 to 10.2 and a Na+ concentration of 3 to 4.8 M, most of the isolates are mesophilic and grow around neutral pH.

Methanogenesis or biomethanation is the formation of methane coupled to energy conservation by microbes known as methanogens. It is the fourth and final stage of anaerobic digestion. Organisms capable of producing methane for energy conservation have been identified only from the domain Archaea, a group phylogenetically distinct from both eukaryotes and bacteria, although many live in close association with anaerobic bacteria. The production of methane is an important and widespread form of microbial metabolism. In anoxic environments, it is the final step in the decomposition of biomass. Methanogenesis is responsible for significant amounts of natural gas accumulations, the remainder being thermogenic.

Archaeoglobus is a genus of the phylum Euryarchaeota. Archaeoglobus can be found in high-temperature oil fields where they may contribute to oil field souring.

Methanopyrus is a genus of methanogen, with a single described species, Methanopyrus kandleri. It is a rod-shaped hyperthermophile, discovered on the wall of a black smoker from the Gulf of California at a depth of 2,000 m, at temperatures of 84–110 °C. Strain 116 was discovered in black smoker fluid of the Kairei hydrothermal field; it can survive and reproduce at 122 °C. M. kandleri also requires a high ionic concentration in order for growth and cellular activity. Due to the species' high resilience and extreme environment, M. kandleri is also classified as an extremophile. It lives in a hydrogen–carbon dioxide rich environment, and like other methanogens reduces the latter to methane. It is placed among the Euryarchaeota, in its own class.

<i>Methanosarcina</i> Genus of archaea

Methanosarcina is a genus of euryarchaeote archaea that produce methane. These single-celled organisms are known as anaerobic methanogens that produce methane using all three metabolic pathways for methanogenesis. They live in diverse environments where they can remain safe from the effects of oxygen, whether on the earth's surface, in groundwater, in deep sea vents, and in animal digestive tracts. Methanosarcina grow in colonies.

Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.

<span class="mw-page-title-main">Wood–Ljungdahl pathway</span> A set of biochemical reactions used by some bacteria

The Wood–Ljungdahl pathway is a set of biochemical reactions used by some bacteria. It is also known as the reductive acetyl-coenzyme A (acetyl-CoA) pathway. This pathway enables these organisms to use hydrogen as an electron donor, and carbon dioxide as an electron acceptor and as a building block for biosynthesis.

<i>Methanobacterium</i> Genus of archaea

Methanobacterium is a genus of the Methanobacteria class in the Archaea kingdom, which produce methane as a metabolic byproduct. Despite the name, this genus belongs not to the bacterial domain but the archaeal domain. Methanobacterium are nonmotile and live without oxygen, which is toxic to them, and they only inhabit anoxic environments.

<i>Methanobrevibacter smithii</i> Species of archaeon

Methanobrevibacter smithii is the predominant methanogenic archaeon in the microbiota of the human gut. M. smithii has a coccobacillus shape. It plays an important role in the efficient digestion of polysaccharides (complex sugars) by consuming the end products of bacterial fermentation (H2, acetate, formate to some extant). M. smithii is a hydrogenotrophic methanogen that utilizes hydrogen by combining it with carbon dioxide to form methane. The removal of hydrogen by M. smithii is thought to allow an increase in the extraction of energy from nutrients by shifting bacterial fermentation to more oxidized end products.

<span class="mw-page-title-main">Archaea</span> Domain of organisms

Archaea is a domain of organisms. Traditionally, Archaea only included its prokaryotic members, but this sense has been found to be paraphyletic, as eukaryotes are now known to have evolved from archaea. Even though the domain Archaea includes eukaryotes, the term "archaea" in English still generally refers specifically to prokaryotic members of Archaea. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

Thermococcus celer is a Gram-negative, spherical-shaped archaeon of the genus Thermococcus. The discovery of T. celer played an important role in rerooting the tree of life when T. celer was found to be more closely related to methanogenic Archaea than to other phenotypically similar thermophilic species. T. celer was the first archaeon discovered to house a circularized genome. Several type strains of T. celer have been identified: Vu13, ATCC 35543, and DSM 2476.

Methanocaldococcus jannaschii is a thermophilic methanogenic archaean in the class Methanococci. It was the first archaeon, and third organism, to have its complete genome sequenced. The sequencing identified many genes unique to the archaea. Many of the synthesis pathways for methanogenic cofactors were worked out biochemically in this organism, as were several other archaeal-specific metabolic pathways.

In the taxonomy of microorganisms, the Methanothrix is a genus of methanogenic archaea within the Euryarchaeota. Methanothrix cells were first isolated from a mesophilic sewage digester but have since been found in many anaerobic and aerobic environments. Methanothrix were originally understood to be obligate anaerobes that can survive exposure to high concentrations of oxygen, but recent studies have shown at least one Candidatus operational taxonomic unit proposed to be in the Methanothrix genus not only survives but remains active in oxic soils. This proposed species, Ca. Methanothrix paradoxum, is frequently found in methane-releasing ecosystems and is the dominant methanogen in oxic soils.

The archaellum is a unique structure on the cell surface of many archaea that allows for swimming motility. The archaellum consists of a rigid helical filament that is attached to the cell membrane by a molecular motor. This molecular motor – composed of cytosolic, membrane, and pseudo-periplasmic proteins – is responsible for the assembly of the filament and, once assembled, for its rotation. The rotation of the filament propels archaeal cells in liquid medium, in a manner similar to the propeller of a boat. The bacterial analog of the archaellum is the flagellum, which is also responsible for their swimming motility and can also be compared to a rotating corkscrew. Although the movement of archaella and flagella is sometimes described as "whip-like", this is incorrect, as only cilia from Eukaryotes move in this manner. Indeed, even "flagellum" is a misnomer, as bacterial flagella also work as propeller-like structures.

Methanococcoides burtonii is a methylotrophic methanogenic archaeon first isolated from Ace Lake, Antarctica. Its type strain is DSM 6242.

Hydrogenotrophs are organisms that are able to metabolize molecular hydrogen as a source of energy.

Methanocaldococcussp. FS406-22 is an archaea in the genus Methanocaldococcus. It is an anaerobic, piezophilic, diazotrophic, hyperthermophilic marine archaeon. This strain is notable for fixing nitrogen at the highest known temperature of nitrogen fixers recorded to date. The 16S rRNA gene of Methanocaldococcus sp. FS406-22, is almost 100% similar to that of Methanocaldococcus jannaschii, a non-nitrogen fixer.

In enzymology, a formylmethanofuran dehydrogenase (EC 1.2.99.5) is an enzyme that catalyzes the chemical reaction:

Formatotrophs are organisms that can assimilate formate or formic acid to use as a carbon source or for reducing power. Some authors classify formatotrophs as one of the five trophic groups of methanogens, which also include hydrogenotrophs, acetotrophs, methylotrophs, and alcoholotrophs. Formatotrophs have garnered attention for applications in biotechnology as part of a "formate bioeconomy" in which synthesized formate could be used as a nutrient for microoganisms. Formate can be electrochemically synthesized from CO2 and renewable energy, and formatotrophs may be genetically modified to enhance production of biochemical products to be used as biofuels. Technical limitations in culturing formatotrophs have limited the discovery of natural formatotrophs and impeded research on their formate-metabolizing enzymes, which are of interest for applications in carbon sequestration and astrobiology.

<span class="mw-page-title-main">Wolfe cycle</span> Methanogenic pathway

The Wolfe Cycle is a methanogenic pathway used by archaea; the archaeon takes H2 and CO2 and cycles them through a various intermediates to create methane. The Wolfe Cycle is modified in different orders and classes of archaea as per the resource availability and requirements for each species, but it retains the same basic pathway. The pathway begins with the reducing carbon dioxide to formylmethanofuran. The last step uses heterodisulfide reductase (Hdr) to reduce heterodisulfide into Coenzyme B and Coenzyme M using Fe4S4 clusters. Evidence suggests this last step goes hand-in-hand with the first step, and feeds back into it, creating a cycle. At various points in the Wolfe Cycle, intermediates that are formed are taken out of the cycle to be used in other metabolic processes. Since intermediates are being taken out at various points in the cycle, there is also a replenishing (anaplerotic) reaction that feeds into the Wolfe cycle, this is to regenerate necessary intermediates for the cycle to continue. Overall, including the replenishing reaction, the Wolfe Cycle has a total of nine steps. While Obligate reducing methanogens perform additional steps to reduce CO2 to .

References

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