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#Demethylation of methyl-S-CoM to form methane and generate additional energy via subsequent reduction of byproducts with H<sub>2</sub><ref>{{cite journal | vauthors = Kaster AK, Moll J, Parey K, Thauer RK | title = Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 7 | pages = 2981–2986 | date = February 2011 | pmid = 21262829 | pmc = 3041090 | doi = 10.1073/pnas.1016761108 | doi-access = free | bibcode = 2011PNAS..108.2981K }}</ref>
#Demethylation of methyl-S-CoM to form methane and generate additional energy via subsequent reduction of byproducts with H<sub>2</sub><ref>{{cite journal | vauthors = Kaster AK, Moll J, Parey K, Thauer RK | title = Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 7 | pages = 2981–2986 | date = February 2011 | pmid = 21262829 | pmc = 3041090 | doi = 10.1073/pnas.1016761108 | doi-access = free | bibcode = 2011PNAS..108.2981K }}</ref>


=== Nitrogen Metabolism[edit] ===
=== Nitrogen Metabolism ===
''M. maripaludis'' utilizes three sources of nitrogen: ammonia, alanine, and dinitrogen with ammonia.<ref name=":2">{{Cite journal |last=Goyal |first=Nishu |last2=Zhou |first2=Zhi |last3=Karimi |first3=Iftekhar A. |date=2016-06-10 |title=Metabolic processes of Methanococcus maripaludis and potential applications |url=https://doi.org/10.1186/s12934-016-0500-0 |journal=Microbial Cell Factories |volume=15 |issue=1 |pages=107 |doi=10.1186/s12934-016-0500-0 |issn=1475-2859 |pmc=PMC4902934 |pmid=27286964}}</ref> 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.<ref name=":2" />
''M. maripaludis'' utilizes three sources of nitrogen: ammonia, alanine, and dinitrogen with ammonia.<ref name=":2">{{Cite journal |last=Goyal |first=Nishu |last2=Zhou |first2=Zhi |last3=Karimi |first3=Iftekhar A. |date=2016-06-10 |title=Metabolic processes of Methanococcus maripaludis and potential applications |url=https://doi.org/10.1186/s12934-016-0500-0 |journal=Microbial Cell Factories |volume=15 |issue=1 |pages=107 |doi=10.1186/s12934-016-0500-0 |issn=1475-2859 |pmc=PMC4902934 |pmid=27286964}}</ref> 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.<ref name=":2" />


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Free  <chem>N2</chem>fixation is well established in ''M. maripaludis. M. maripaludis'' contains a multiprotein nitrogen complex containing a Fe protein and a MoFe.<ref name=":2" />  The ferredoxin is reduced and reduces the oxidized Fe stripping the Fe of its electrons in the presence of <chem>N2</chem>. The now reduced Fe protein is then oxidized by ATP and reducing the MoFe protein.<ref name=":2" />  The MoFe protein then reduces <chem>N2</chem> to ammonia. This reductive step requires high energy to be carried out as it uses the electrons from the reduced ferredoxinn. <chem>N2</chem> 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.<ref name=":2" />
Free  <chem>N2</chem>fixation is well established in ''M. maripaludis. M. maripaludis'' contains a multiprotein nitrogen complex containing a Fe protein and a MoFe.<ref name=":2" />  The ferredoxin is reduced and reduces the oxidized Fe stripping the Fe of its electrons in the presence of <chem>N2</chem>. The now reduced Fe protein is then oxidized by ATP and reducing the MoFe protein.<ref name=":2" />  The MoFe protein then reduces <chem>N2</chem> to ammonia. This reductive step requires high energy to be carried out as it uses the electrons from the reduced ferredoxinn. <chem>N2</chem> 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.<ref name=":2" />


=== Non-Oxidative Pentose Phosphate Pathway (NOPPP)[edit] ===
=== Non-Oxidative Pentose Phosphate Pathway (NOPPP) ===
The pentose phosphate pathway is essential in ''M. maripaludis'' to make nucleotides and nucleic acids.<ref name=":2" />  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.<ref name=":2" />  Four enzymes are used in this conversion: Transketoloase, ribulose-phosphate 3-epimerase, ribose-r-phosphate isomerase, and translaldolase.
The pentose phosphate pathway is essential in ''M. maripaludis'' to make nucleotides and nucleic acids.<ref name=":2" />  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.<ref name=":2" />  Four enzymes are used in this conversion: Transketoloase, ribulose-phosphate 3-epimerase, ribose-r-phosphate isomerase, and translaldolase.


Revision as of 23:07, 17 March 2024

Methanococcus maripaludis
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] 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][3] M. maripaludis also has a sequenced genome consisting of around 1.7 Mbp with over 1,700 identified protein-coding genes.[4] In ideal conditions, M. maripaludis grows quickly and can double every two hours.[3]

Metabolism

The metabolic landscape of M. maripaludis consists of eight major subsystems:[3]

Amino Acid Metabolism

M. maripaludis uses carbon dioxide and acetate as substrates for amino acid biosynthesis.[3] Each of these substrates can produce Acetyl-CoA through various mechanisms.[3] Using acetate, Acetyl-CoA is synthesized from the AMP-forming acetate CoA ligase.[3] 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.[3] Acetyl-CoA then acts as a precursor to pyruvate, which promotes methanogenesis and alanine biosynthesis.[3] 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.[3]

Glycolysis/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.[3] 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.[3] M. maripaludis is also capable of synthesizing glycogen.[3] 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.[3]

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.[5] 7 different hydrogenases are present in M. maripaludis that allow for the usage of H2 as an electron donor to reduce CO2.[3] 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.[6]

Methanogenesis in M. maripaludis occurs in the following steps:

  1. Reduction of CO2 via methanofuran and reduced ferredoxins[7]
  2. Oxidation and subsequent reduction of the coenzyme F420 in the presence of H2[8][7]
  3. Transfer of methyl group from methyl-THMPT to coenzyme M (HS-CoM), driving translocation of 2Na+ across membrane to strengthen the proton gradient[9]
  4. Demethylation of methyl-S-CoM to form methane and generate additional energy via subsequent reduction of byproducts with H2[10]

Nitrogen Metabolism

M. maripaludis utilizes three sources of nitrogen: ammonia, alanine, and dinitrogen with ammonia.[11] 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.[11]

M. maripaludis utilizes alanine racemase and alanine permease for alanine uptake.[11]  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. [12]

Free  fixation is well established in M. maripaludis. M. maripaludis contains a multiprotein nitrogen complex containing a Fe protein and a MoFe.[11]  The ferredoxin is reduced and reduces the oxidized Fe stripping the Fe of its electrons in the presence of . The now reduced Fe protein is then oxidized by ATP and reducing the MoFe protein.[11]  The MoFe protein then reduces to ammonia. This reductive step requires high energy to be carried out as it uses the electrons from the reduced ferredoxinn. 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.[11]

Non-Oxidative Pentose Phosphate Pathway (NOPPP)

The pentose phosphate pathway is essential in M. maripaludis to make nucleotides and nucleic acids.[11]  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.[11]  Four enzymes are used in this conversion: Transketoloase, ribulose-phosphate 3-epimerase, ribose-r-phosphate isomerase, and translaldolase.

Cell structure

The cell wall of Methanococcus maripaludis has an S-layer that does not contain peptidoglycan, which helps to identify its domain as Archaea.[3] 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. [13] These cells use both flagella and pili to attach to surfaces, meaning that if they encounter a desirable environment, they can remain there.[13]

Genetic characteristics

Methanococcus maripaludis is one of four hydrogenotrophic methanogens, along with Methanocaldococcus jannaschii, Methanothermobacter thermautotrophicus, and Methanopyrus kandleri, to have its genome sequenced.[3] Of these four, Methanocaldococcus jannaschii is the closest living, known relative of M. maripaludis. M. maripaludis, like many other archaea, has one single circular chromosome.[3] Of its 1,722 protein coding genes, 835 ORFs, or open reading frames, have unknown functions, and 129 ORFs are unique to M. maripaludis.[3] The sequenced genome also revealed about 48 protein transporter systems, largely dominated by ABC transporters followed by iron transporters.[4] According to the number of BlastP hits, or similar protein sequences identified by the Basic Local Alignment Search Tool (BLAST), in the genome sequence, M. maripaludis is similar to most other methanogens.[3] However, M. maripaludis is missing certain features present in most methanogens, such as the ribulose bisphosphate carboxylase enzyme.[3]

Environmental roles

Methanogens play important roles in waste water treatment, carbon conversion, hydrogen production, and many other environmental processes.[3] In terms of waste water treatment, methanogens have been used to anaerobically degrade waste into methane utilizing a symbiotic relationship with syntrophic bacteria.[3] M. maripaludis has similar potential applications, but an issue with using any methanogen for biomethane production is the need for high amounts of hydrogen.[3]

References

  1. ^ Populations of methanogenic bacteria in a georgia salt marsh. Applied and Environmental Microbiology. May 1988;54(5):1151–7. doi:10.1128/aem.54.5.1151-1157.1988. PMID 16347628.
  2. ^ a b Jones WJ, Paynter MJ, Gupta R (1983-08-01). "Characterization of Methanococcus maripaludis sp. nov., a new methanogen isolated from salt marsh sediment". Archives of Microbiology. 135 (2): 91–97. doi:10.1007/BF00408015. ISSN 1432-072X.
  3. ^ a b c d e f g h i j k l m n o p q r s t u v w Goyal N, Zhou Z, Karimi IA (June 2016). "Metabolic processes of Methanococcus maripaludis and potential applications". Microbial Cell Factories. 15 (1): 107. doi:10.1186/s12934-016-0500-0. PMC 4902934. PMID 27286964.
  4. ^ a b Hendrickson EL, Kaul R, Zhou Y, Bovee D, Chapman P, Chung J, Conway de Macario E, Dodsworth JA, Gillett W, Graham DE, Hackett M, Haydock AK, Kang A, Land ML, Levy R (2004-10-15). "Complete Genome Sequence of the Genetically Tractable Hydrogenotrophic Methanogen Methanococcus maripaludis". Journal of Bacteriology. 186 (20): 6956–6969. doi:10.1128/JB.186.20.6956-6969.2004. ISSN 0021-9193. PMC 522202. PMID 15466049.
  5. ^ Escalante-Semerena JC, Rinehart KL, Wolfe RS (August 1984). "Tetrahydromethanopterin, a carbon carrier in methanogenesis". The Journal of Biological Chemistry. 259 (15): 9447–9455. doi:10.1016/s0021-9258(17)42721-9. PMID 6547718.
  6. ^ Lohner ST, Deutzmann JS, Logan BE, Leigh J, Spormann AM (August 2014). "Hydrogenase-independent uptake and metabolism of electrons by the archaeon Methanococcus maripaludis". The ISME Journal. 8 (8): 1673–1681. Bibcode:2014ISMEJ...8.1673L. doi:10.1038/ismej.2014.82. PMC 4817615. PMID 24844759.
  7. ^ a b Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R (August 2008). "Methanogenic archaea: ecologically relevant differences in energy conservation". Nature Reviews. Microbiology. 6 (8): 579–591. doi:10.1038/nrmicro1931. PMID 18587410. S2CID 32698014.
  8. ^ Mukhopadhyay B, Stoddard SF, Wolfe RS (February 1998). "Purification, regulation, and molecular and biochemical characterization of pyruvate carboxylase from Methanobacterium thermoautotrophicum strain deltaH". The Journal of Biological Chemistry. 273 (9): 5155–5166. doi:10.1074/jbc.273.9.5155. PMID 9478969.
  9. ^ Kengen SW, Daas PJ, Duits EF, Keltjens JT, van der Drift C, Vogels GD (February 1992). "Isolation of a 5-hydroxybenzimidazolyl cobamide-containing enzyme involved in the methyltetrahydromethanopterin: coenzyme M methyltransferase reaction in Methanobacterium thermoautotrophicum". Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology. 1118 (3): 249–260. doi:10.1016/0167-4838(92)90282-i. PMID 1737047.
  10. ^ Kaster AK, Moll J, Parey K, Thauer RK (February 2011). "Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea". Proceedings of the National Academy of Sciences of the United States of America. 108 (7): 2981–2986. Bibcode:2011PNAS..108.2981K. doi:10.1073/pnas.1016761108. PMC 3041090. PMID 21262829.
  11. ^ a b c d e f g h Goyal N, Zhou Z, Karimi IA (2016-06-10). "Metabolic processes of Methanococcus maripaludis and potential applications". Microbial Cell Factories. 15 (1): 107. doi:10.1186/s12934-016-0500-0. ISSN 1475-2859. PMC 4902934. PMID 27286964.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  12. ^ "Definition of PERMEASE". www.merriam-webster.com. Retrieved 2024-03-17.
  13. ^ a b Jarrell KF, Stark M, Nair DB, Chong JP (June 2011). "Flagella and pili are both necessary for efficient attachment of Methanococcus maripaludis to surfaces". FEMS Microbiology Letters. 319 (1): 44–50. doi:10.1111/j.1574-6968.2011.02264.x. PMID 21410509. S2CID 36895781.

Further reading

  • Haydock AK, Porat I, Whitman WB, Leigh JA (September 2004). "Continuous culture of Methanococcus maripaludis under defined nutrient conditions". FEMS Microbiology Letters. 238 (1): 85–91. doi:10.1016/j.femsle.2004.07.021. PMID 15336407.
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