Characterization of Methanococcus maripaludis sp. nov., a new methanogen isolated from salt marsh sediment

Jones, William J.; Paynter, M. J. B.; Gupta, Ramesh C.

doi:10.1007/bf00408015

Cited by 202 publications

(140 citation statements)

References 25 publications

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“…Antisera to M. voltaei PST, M. rnaripaludis JJT, and M. vannielii SBT cross-reacted weakly or not at all with cells of other mesophilic methanococci (Table 1). This finding was in agreement with the data of Jones et al (24) and indicated that there was a great deal of antigenic heterogeneity. An exception to this observation was that cells of M. deltae and a few other strains of autotrophic methanococci reacted strongly with the S probe of M. maripaludis but showed no a Data from reference 44.…”

Section: Resultssupporting

confidence: 93%

“…Five species, Methanococcus vannielii, Methanococcus voltaei, Methanococcus maripaludis, Methanococcus deltae, and "Methanococcus aeolicus," are mesophilic, and three species, Methanococcus ("Methanothermococcus") thermolithotrophicus, Methanococcus ("Methanoignis") igneus, and Methanococcus ("Methanocaldococcus~7) jannaschii (4) (proposed genus names in parentheses), are thermophilic. The relationships of all of the mesophilic species except "M. aeolicus" have been determined by 16s rRNA cataloging studies (24). Therefore, to establish the phylogenetic relationships of the mesophilic species in accordance with the recommendations of the International Committee on Systematic Bacteriology Subcommittee for Taxonomy of Methanogenic Bacteria (3), the levels of sequence similarity of nearly complete 16s rRNA sequences and DNA-DNA hybridization values were determined.…”

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confidence: 99%

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Phylogeny and Taxonomy of Mesophilic Methanococcus spp. and Comparison of rRNA, DNA Hybridization, and Phenotypic Methods

Keswani

Orkand

Premachandran

et al. 1996

International Journal of Systematic Bacteriology

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The phylogeny and taxonomy of the mesophilic methane-producing archaea of the order Methanococcales were examined by DNA relatedness, 16s rRNA sequence analysis, cellular protein pattern, and phenotypic methods. The mesophilic species Methanococcus maripaludis, Methanococcus vannielii, Methanococcus voltaei, and 44Methanococcus aeolicus" formed a deep group with 5 to 30% DNA relatedness and 92 to 96% 16s rRNA sequence similarity. Twenty-two additional isolates and Methanococcus deltae were similar to the type strain of either M. voltaei or M. maripaludis. Two isolates, strains A2 and A3, exhibited 37% DNA relatedness and 99.2% 16s rRNA sequence similarity to M. voltaei PST (T = type strain). In the absence of phenotypic differences, these organisms were assigned to M. voltaei. Similarly, four autotrophic isolates, strains C5, C6, C7, and C8, exhibited 54 to 69% DNA relatedness and 99.2% 16s rRNA sequence similarity to M. maripaludis JJT and were assigned to M. maripaludis. While these isolates were sufficiently genetically diverse to justify classification in novel species, few differences were apparent in the phenotypic properties available for measurement. Thus, the phenotypic properties of these lithotrophic archaea were highly conserved and poor indicators of genetic diversity. Partial sequencing of about 200 bases of both the 16s and 23s rRNAs of the isolates demonstrated allelic diversity within methanococcal species. This allelic diversity did not correlate with diversity measured by DNA relatedness, cellular protein pattern, and other methods. Similarly, antisera to whole cells of the type strains did not cross-react strongly to whole cells of strains that were genetically similar, and serological cross-reactivity was not a useful taxonomic method for methanococci. Lastly, on the basis of the results of 16s rRNA sequence analyses and biochemical data, the ancestor of the mesophilic methanococci may have been an autotrophic thermophile.The genus Methanococcus belongs to the family Methanococcaceae and the order Methanococcales, which is one of five orders within the Archaea that include methanogenic bacteria (3). The order Methanococcales is composed of coccoid methane-producing bacteria of marine origin. Distinctive features of this group include rapid growth at either mesophilic or thermophilic temperatures, cell envelopes composed of protein S-layers, and a nutritional requirement for selenium (6,18,23,44,45). To date, eight Methanococcales species belonging to two families and four genera have been described. Five species, Methanococcus vannielii, Methanococcus voltaei, Methanococcus maripaludis, Methanococcus deltae, and "Methanococcus aeolicus," are mesophilic, and three species, Methanococcus ("Methanothermococcus") thermolithotrophicus, Methanococcus ("Methanoignis") igneus, and Methanococcus ("Methanocaldococcus~7) jannaschii (4) (proposed genus names in parentheses), are thermophilic. The relationships of all of the mesophilic species except "M. aeolicus" have been determined by 16s rRNA catalog...

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Section: Resultssupporting

confidence: 93%

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confidence: 99%

Phylogeny and Taxonomy of Mesophilic Methanococcus spp. and Comparison of rRNA, DNA Hybridization, and Phenotypic Methods

Keswani

Orkand

Premachandran

et al. 1996

International Journal of Systematic Bacteriology

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“…It is tempting to suggest that it is also the sulfur source in vivo. Free sulfide has been shown to be present at relatively high concentrations within thermophilic archaea (13) and participate in [Fe-S] cluster assembly as well as biosynthesis of methionine (14), thiamin thiazole (15), and U8-tRNA thiolation (16).…”

Section: Discussionmentioning

confidence: 99%

Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster

Arragain

Bimaï

Legrand

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Sulfur is present in several nucleosides within tRNAs. In particular, thiolation of the universally conserved methyl-uridine at position 54 stabilizes tRNAs from thermophilic bacteria and hyperthermophilic archaea and is required for growth at high temperature. The simple nonredox substitution of the C2-uridine carbonyl oxygen by sulfur is catalyzed by tRNA thiouridine synthetases called TtuA. Spectroscopic, enzymatic, and structural studies indicate that TtuA carries a catalytically essential [4Fe-4S] cluster and requires ATP for activity. A series of crystal structures shows that (i) the cluster is ligated by only three cysteines that are fully conserved, allowing the fourth unique iron to bind a small ligand, such as exogenous sulfide, and (ii) the ATP binding site, localized thanks to a proteinbound AMP molecule, a reaction product, is adjacent to the cluster. A mechanism for tRNA sulfuration is suggested, in which the unique iron of the catalytic cluster serves to bind exogenous sulfide, thus acting as a sulfur carrier.T he cellular translation machinery contains essential components such as tRNAs. To achieve their function, they feature a great variety of well-conserved posttranscriptional chemical modifications. Sulfur is present in several of these modified nucleosides: thiouridine and derivatives (s 4 U8, s 2 U34, and m 5 s 2 U54), 2-thioadenosine derivatives (ms 2 i 6 A37 and ms 2 t 6 A37), and 2-thiocytidine (s 2 C32). However, mechanisms of sulfur insertion into tRNAs are largely unknown, and the enzymes responsible for these reactions are incompletely characterized. Whereas redox conversion of a C-H to a C-S bond (synthesis of ms 2 i 6 A37 and ms 2 t 6 A37) depends on redox enzymes from the Radical-S-adenosyl-L-methionine iron-sulfur enzyme family, simple nonredox conversion of C = O to C = S group (synthesis of s 2 U34 and s 4 U8) is not expected to require such redox clusters. Intriguingly, we recently discovered that the ATPdependent formation of s 2 C32 in some tRNAs is catalyzed by an iron-sulfur enzyme, TtcA (1). However, the role of its cluster has not been defined. In the same superfamily, TtuA enzymes catalyze the C2-thiolation of uridine 54 in the T loop of thermophilic tRNAs (Fig. 1A), allowing stabilization of tRNAs at high temperature in thermophilic microorganisms. Sequences analysis shows that they share conserved cysteines and ATP binding motif (Fig. S1). Here, we report a detailed biochemical and structural characterization of TtuA that shows the presence of a [4Fe-4S] cluster essential for activity. The crystal structures of Pyrococcus horikoshii TtuA (PhTtuA) show that the cluster, chelated by only three cysteines, is adjacent to the ATP binding site. The presence of electron density near the fourth iron, nonbonded to the protein, indicates that the cluster can bind an exogenous substrate. We propose that thiolation occurs via sulfur binding to the cluster and transfer to the tRNA substrate. The fact that the catalytic [4Fe-4S] cluster serves as a sulfur carrier during a nonredox ...

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“…Instead, it is derived from sulfide, which is abundant in the anaerobic environment where the organism was isolated (11). This discovery also sheds light on the Fe-S cluster biogenesis in other organisms living in sulfide-rich environments and early life forms on the anoxic earth when sulfide was abundant.…”

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confidence: 83%

Cysteine Is Not the Sulfur Source for Iron-Sulfur Cluster and Methionine Biosynthesis in the Methanogenic Archaeon Methanococcus maripaludis

Liu

Sieprawska-Lupa

Whitman

et al. 2010

Journal of Biological Chemistry

111

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Three multiprotein systems are known for iron-sulfur (Fe-S) cluster biogenesis in prokaryotes and eukaryotes as follows: the NIF (nitrogen fixation), the ISC (iron-sulfur cluster), and the SUF (mobilization of sulfur) systems. In all three, cysteine is the physiological sulfur source, and the sulfur is transferred from cysteine desulfurase through a persulfidic intermediate to a scaffold protein. However, the biochemical nature of the sulfur source for Fe-S cluster assembly in archaea is unknown, and many archaea lack homologs of cysteine desulfurases. Methanococcus maripaludis is a methanogenic archaeon that contains a high amount of protein-bound Fe-S clusters (45 nmol/mg protein). Cysteine in this archaeon is synthesized primarily via the tRNA-dependent SepRS/SepCysS pathway. When a ⌬sepS mutant (a cysteine auxotroph) was grown with 34 S-labeled sulfide and unlabeled cysteine, <8% of the cysteine, >92% of the methionine, and >87% of the sulfur in the Fe-S clusters in proteins were labeled, suggesting that the sulfur in methionine and Fe-S clusters was derived predominantly from exogenous sulfide instead of cysteine. Therefore, this investigation challenges the concept that cysteine is always the sulfur source for Fe-S cluster biosynthesis in vivo and suggests that Fe-S clusters are derived from sulfide in those organisms, which live in sulfiderich habitats.

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Characterization of Methanococcus maripaludis sp. nov., a new methanogen isolated from salt marsh sediment

Cited by 202 publications

References 25 publications

Phylogeny and Taxonomy of Mesophilic Methanococcus spp. and Comparison of rRNA, DNA Hybridization, and Phenotypic Methods

Phylogeny and Taxonomy of Mesophilic Methanococcus spp. and Comparison of rRNA, DNA Hybridization, and Phenotypic Methods

Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster

Cysteine Is Not the Sulfur Source for Iron-Sulfur Cluster and Methionine Biosynthesis in the Methanogenic Archaeon Methanococcus maripaludis

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