User:Eesakguee/Methanococcus maripaludis

Methanococcus maripaludis is a species of methanogenic archaea found in marine environments, predominantly salt marshes. M. maripaludis is a non-pathogenic, gram-negative, weakly motile, non-spore-forming and strictly anaerobic mesophile with a pleomorphic coccoid-rod shape of 1.2 by 1.6 μm, in average size. The genome of M. maripaludis consists of 1,661,137 bp and has been sequenced, leading to the identification of over 1,700 protein-coding genes. In ideal conditions, M. maripaludis grows quickly and can double every two hours.

Metabolism[edit]

The metabolic landscape of M. maripaludis consists of eight major subsystems, providing pathways for energy for growth from carbon sources:

• Amino Acid Metabolism
• Glucose/Glycogen Metabolism
• Glycolysis
• Methanogenesis
• Nitrogen Metabolism
• Non-Oxidative Pentose Phosphate Pathway (NOPPP)
• Nucleotide Metabolism
• Reductive Citric Acid (TCA) Cycle

Amino Acid Metabolism

M. maripaludis uses carbon dioxide and acetate as substrates for amino acid biosynthesis. Each of these substrates can produce Acetyl-CoA through various mechanisms. Using acetate, Acetyl-CoA is synthesized from the AMP-forming acetate CoA ligase. Using carbon dioxide, M. maripaludis can generate Acetyl-CoA from carbon monoxide, produced from the reduction of carbon dioxide, and methyl-THMPT, produced as an intermediate of methanogenesis during biosynthesis. Acetyl-CoA then acts as a precursor to pyruvate, which promotes methanogenesis and alanine biosynthesis. 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.

Glucose/Glycogen Metabolism

M. maripaludis has a modified Embden Meyerhof-Parnas (EMP) pathway, also known as glycolysis, responsible for the catabolic breakdown of glucose into pyruvate. 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. M. maripaludis is also capable of synthesizing glycogen. 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.

Methanogenesis

In M. maripaludis, the primary carbon source for methanogenesis is carbon dioxide, although alternatives such as formate are also used. Though all methanogens utilize 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 different hydrogenases are present in M. maripaludis that allow for the usage of H₂ as an electron donor to reduce CO_2. 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.

Methanogenesis in M. maripaludis occurs in the following steps:

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

Nitrogen Metabolism

M. maripaludis utilizes three sources of nitrogen: ammonia, alanine, and dinitrogen with ammonia. Nitrogen assimilation occurs in the bacteria through ammonia. Nitrogen assimilation is 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.

M. maripaludis utilizes alanine racemase and alanine permease for alanine uptake. 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.

Free ${\ce {N2}}$ fixation is well established in M. maripaludis. M. maripaludis contains a multiprotein nitrogen complex containing a Fe protein and a MoFe. The ferredoxin is reduced and reduces the oxidized Fe stripping the Fe of its electrons in the presence of ${\ce {N2}}$. The now reduced Fe protein is then oxidized by ATP and reducing the MoFe protein. The MoFe protein then reduces ${\ce {N2}}$ to ammonia. This reductive step requires high energy to be carried out as it uses the electrons from the reduced ferredoxinn. ${\ce {N2}}$ fixation is unfavorable in M. maripaludis because of the high energy demand so it is common for a cell to not activate this fixation when ammonia and alanine are available.

Non-Oxidative Pentose Phosphate Pathway (NOPPP)

The pentose phosphate pathway is essential in M. maripaludis to make nucleotides and nucleic acids. The non-oxidative pentose phosphate pathway (NOPPP) is regulated and used through substrate availability. In M. maripaludis Ribulose-5-phosphate will be converted to Erythrose-4-phosphate and Fructose-6-phosphate. Four enzymes are used in this conversion: Transketoloase, ribulose-phosphate 3-epimerase, ribose-r-phosphate isomerase, and translaldolase.

Reductive Citric Acid (RTCA) Cycle

Tricarboxylic Acid Cycle, serves as a central metabolic pathway in aerobic organisms, playing an essential role in energy production and biosynthesis by generating electron carries such as NADH and FAD. This is performed by oxidizing acetyl-CoA derived from various nutrients, complex carbon molecules, to CO₂ and H₂O.

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

Cell Structure Notes:

Methanococcus maripaludis is a weakly-motile coccus specie of methanogenic archaea of 0.9–1.3 µm diameters. It grows best in conditions of 20°C and 45°C with a pH of 6.5 to 8.0.

Cell structure[edit]

The cell wall of Methanococcus maripaludis has an S-layer that does not contain peptidoglycan, which helps to identify its domain as Archaea. The S-layer is made of glycoproteins and encloses the whole cell. It protects the cell and is its direct interaction with the environment. The S-layer gives the archaea cell a stabilization barrier being resistant to environmental changes.

M. maripaludis contains flagella for motility and pili. The pili's function for this microbe is not fully known but could include cellular attachment, motility, and biofilm formation.

Genetic characteristics[edit]

The sequenced genome also revealed about 48 protein transporter systems, largely dominated by ABC transporters followed by iron transporters.