1
|
Barrera-Rojas J, Gurubel-Tun KJ, Ríos-Castro E, López-Méndez MC, Sulbarán-Rangel B. An Initial Proteomic Analysis of Biogas-Related Metabolism of Euryarchaeota Consortia in Sediments from the Santiago River, México. Microorganisms 2023; 11:1640. [PMID: 37512813 PMCID: PMC10384328 DOI: 10.3390/microorganisms11071640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
In this paper, sediments from the Santiago River were characterized to look for an alternative source of inoculum for biogas production. A proteomic analysis of methane-processing archaea present in these sediments was carried out. The Euryarchaeota superkingdom of archaea is responsible for methane production and methane assimilation in the environment. The Santiago River is a major river in México with great pollution and exceeded recovery capacity. Its sediments could contain nutrients and the anaerobic conditions for optimal growth of Euryarchaeota consortia. Batch bioreactor experiments were performed, and a proteomic analysis was conducted with current database information. The maximum biogas production was 266 NmL·L-1·g VS-1, with 33.34% of methane, and for proteomics, 3206 proteins were detected from 303 species of 69 genera. Most of them are metabolically versatile members of the genera Methanosarcina and Methanosarcinales, both with 934 and 260 proteins, respectively. These results showed a diverse euryarcheotic species with high potential to methane production. Although related proteins were found and could be feeding this metabolism through the methanol and acetyl-CoA pathways, the quality obtained from the biogas suggests that this metabolism is not the main one in carbon use, possibly the sum of several conditions including growth conditions and the pollution present in these sediments.
Collapse
Affiliation(s)
- Jesús Barrera-Rojas
- Department of Water and Energy, Campus Tonalá, University of Guadalajara, Tonalá 45425, Mexico
| | - Kelly Joel Gurubel-Tun
- Department of Water and Energy, Campus Tonalá, University of Guadalajara, Tonalá 45425, Mexico
| | - Emmanuel Ríos-Castro
- Laboratorios Nacionales de Servicios Experimentales, Centro de Investigación y Estudios Avanzados del IPN, Ciudad de México 07000, Mexico
| | - María Cristina López-Méndez
- Wetlands and Environmental Sustainability Laboratory, Division of Graduate Studies and Research, Tecnológico Nacional de México/ITS de Misantla, Veracruz 93850, Mexico
| | - Belkis Sulbarán-Rangel
- Department of Water and Energy, Campus Tonalá, University of Guadalajara, Tonalá 45425, Mexico
| |
Collapse
|
2
|
The pathway for coenzyme M biosynthesis in bacteria. Proc Natl Acad Sci U S A 2022; 119:e2207190119. [PMID: 36037354 PMCID: PMC9457059 DOI: 10.1073/pnas.2207190119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mercaptoethane sulfonate or coenzyme M (CoM) is the smallest known organic cofactor and is most commonly associated with the methane-forming step in all methanogenic archaea but is also associated with the anaerobic oxidation of methane to CO2 in anaerobic methanotrophic archaea and the oxidation of short-chain alkanes in Syntrophoarchaeum species. It has also been found in a small number of bacteria capable of the metabolism of small organics. Although many of the steps for CoM biosynthesis in methanogenic archaea have been elucidated, a complete pathway for the biosynthesis of CoM in archaea or bacteria has not been reported. Here, we present the complete CoM biosynthesis pathway in bacteria, revealing distinct chemical steps relative to CoM biosynthesis in methanogenic archaea. The existence of different pathways represents a profound instance of convergent evolution. The five-step pathway involves the addition of sulfite, the elimination of phosphate, decarboxylation, thiolation, and the reduction to affect the sequential conversion of phosphoenolpyruvate to CoM. The salient features of the pathway demonstrate reactivities for members of large aspartase/fumarase and pyridoxal 5'-phosphate-dependent enzyme families.
Collapse
|
3
|
Murphy CL, Biggerstaff J, Eichhorn A, Ewing E, Shahan R, Soriano D, Stewart S, VanMol K, Walker R, Walters P, Elshahed MS, Youssef NH. Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the phylum. Environ Microbiol 2021; 23:4326-4343. [PMID: 34056821 DOI: 10.1111/1462-2920.15614] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 12/01/2022]
Abstract
We report on the genomic characterization of three novel classes in the phylum Desulfobacterota. One class (proposed name Candidatus 'Anaeroferrophillalia') was characterized by heterotrophic growth capacity, either fermentatively or utilizing polysulfide, tetrathionate or thiosulfate as electron acceptors. In the absence of organic carbon sources, autotrophic growth via the Wood-Ljungdahl (WL) pathway and using hydrogen or Fe(II) as an electron donor is also inferred for members of the 'Anaeroferrophillalia'. The second class (proposed name Candidatus 'Anaeropigmentia') was characterized by its capacity for growth at low oxygen concentration, and the capacity to synthesize the methyl/alkyl carrier CoM, an ability that is prevalent in the archaeal but rare in the bacterial domain. Pigmentation is inferred from the capacity for carotenoid (lycopene) production. The third class (proposed name Candidatus 'Zymogenia') was characterized by fermentative heterotrophic growth capacity, broad substrate range and the adaptation of some of its members to hypersaline habitats. Analysis of the distribution pattern of all three classes showed their occurrence as rare community members in multiple habitats, with preferences for anaerobic terrestrial, freshwater and marine environments over oxygenated (e.g. pelagic ocean and agricultural land) settings. Special preference for some members of the class Candidatus 'Zymogenia' for hypersaline environments such as hypersaline microbial mats and lagoons was observed.
Collapse
Affiliation(s)
- Chelsea L Murphy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - James Biggerstaff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Alexis Eichhorn
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Essences Ewing
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Ryan Shahan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Diana Soriano
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Sydney Stewart
- Department of Animal Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Kaitlynn VanMol
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Ross Walker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Payton Walters
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| |
Collapse
|
4
|
Partovi SE, Mus F, Gutknecht AE, Martinez HA, Tripet BP, Lange BM, DuBois JL, Peters JW. Coenzyme M biosynthesis in bacteria involves phosphate elimination by a functionally distinct member of the aspartase/fumarase superfamily. J Biol Chem 2018; 293:5236-5246. [PMID: 29414784 DOI: 10.1074/jbc.ra117.001234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/23/2018] [Indexed: 11/06/2022] Open
Abstract
For nearly 30 years, coenzyme M (CoM) was assumed to be present solely in methanogenic archaea. In the late 1990s, CoM was reported to play a role in bacterial propene metabolism, but no biosynthetic pathway for CoM has yet been identified in bacteria. Here, using bioinformatics and proteomic approaches in the metabolically versatile bacterium Xanthobacter autotrophicus Py2, we identified four putative CoM biosynthetic enzymes encoded by the xcbB1, C1, D1, and E1 genes. Only XcbB1 was homologous to a known CoM biosynthetic enzyme (ComA), indicating that CoM biosynthesis in bacteria involves enzymes different from those in archaea. We verified that the ComA homolog produces phosphosulfolactate from phosphoenolpyruvate (PEP), demonstrating that bacterial CoM biosynthesis is initiated similarly as the phosphoenolpyruvate-dependent methanogenic archaeal pathway. The bioinformatics analysis revealed that XcbC1 and D1 are members of the aspartase/fumarase superfamily (AFS) and that XcbE1 is a pyridoxal 5'-phosphate-containing enzyme with homology to d-cysteine desulfhydrases. Known AFS members catalyze β-elimination reactions of succinyl-containing substrates, yielding fumarate as the common unsaturated elimination product. Unexpectedly, we found that XcbC1 catalyzes β-elimination on phosphosulfolactate, yielding inorganic phosphate and a novel metabolite, sulfoacrylic acid. Phosphate-releasing β-elimination reactions are unprecedented among the AFS, indicating that XcbC1 is an unusual phosphatase. Direct demonstration of phosphosulfolactate synthase activity for XcbB1 and phosphate β-elimination activity for XcbC1 strengthened their hypothetical assignment to a CoM biosynthetic pathway and suggested functions also for XcbD1 and E1. Our results represent a critical first step toward elucidating the CoM pathway in bacteria.
Collapse
Affiliation(s)
- Sarah E Partovi
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | | | - Andrew E Gutknecht
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | - Hunter A Martinez
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | - Brian P Tripet
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | - Bernd Markus Lange
- the Institute of Biological Chemistry and.,M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164
| | - Jennifer L DuBois
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | | |
Collapse
|
5
|
Expression, Purification, and Characterization of ( R)-Sulfolactate Dehydrogenase (ComC) from the Rumen Methanogen Methanobrevibacter millerae SM9. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2017; 2017:5793620. [PMID: 29234237 PMCID: PMC5695019 DOI: 10.1155/2017/5793620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/19/2017] [Indexed: 12/03/2022]
Abstract
(R)-Sulfolactate dehydrogenase (EC 1.1.1.337), termed ComC, is a member of an NADH/NADPH-dependent oxidoreductase family of enzymes that catalyze the interconversion of 2-hydroxyacids into their corresponding 2-oxoacids. The ComC reaction is reversible and in the biosynthetic direction causes the conversion of (R)-sulfolactate to sulfopyruvate in the production of coenzyme M (2-mercaptoethanesulfonic acid). Coenzyme M is an essential cofactor required for the production of methane by the methyl-coenzyme M reductase complex. ComC catalyzes the third step in the first established biosynthetic pathway of coenzyme M and is also involved in methanopterin biosynthesis. In this study, ComC from Methanobrevibacter millerae SM9 was cloned and expressed in Escherichia coli and biochemically characterized. Sulfopyruvate was the preferred substrate using the reduction reaction, with 31% activity seen for oxaloacetate and 0.2% seen for α-ketoglutarate. Optimal activity was observed at pH 6.5. The apparent KM for coenzyme (NADH) was 55.1 μM, and for sulfopyruvate, it was 196 μM (for sulfopyruvate the Vmax was 93.9 μmol min−1 mg−1 and kcat was 62.8 s−1). The critical role of ComC in two separate cofactor pathways makes this enzyme a potential means of developing methanogen-specific inhibitors for controlling ruminant methane emissions which are increasingly being recognized as contributing to climate change.
Collapse
|
6
|
Borrel G, Parisot N, Harris HMB, Peyretaillade E, Gaci N, Tottey W, Bardot O, Raymann K, Gribaldo S, Peyret P, O’Toole PW, Brugère JF. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics 2014; 15:679. [PMID: 25124552 PMCID: PMC4153887 DOI: 10.1186/1471-2164-15-679] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 07/18/2014] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND A seventh order of methanogens, the Methanomassiliicoccales, has been identified in diverse anaerobic environments including the gastrointestinal tracts (GIT) of humans and other animals and may contribute significantly to methane emission and global warming. Methanomassiliicoccales are phylogenetically distant from all other orders of methanogens and belong to a large evolutionary branch composed by lineages of non-methanogenic archaea such as Thermoplasmatales, the Deep Hydrothermal Vent Euryarchaeota-2 (DHVE-2, Aciduliprofundum boonei) and the Marine Group-II (MG-II). To better understand this new order and its relationship to other archaea, we manually curated and extensively compared the genome sequences of three Methanomassiliicoccales representatives derived from human GIT microbiota, "Candidatus Methanomethylophilus alvus", "Candidatus Methanomassiliicoccus intestinalis" and Methanomassiliicoccus luminyensis. RESULTS Comparative analyses revealed atypical features, such as the scattering of the ribosomal RNA genes in the genome and the absence of eukaryotic-like histone gene otherwise present in most of Euryarchaeota genomes. Previously identified in Thermoplasmatales genomes, these features are presently extended to several completely sequenced genomes of this large evolutionary branch, including MG-II and DHVE2. The three Methanomassiliicoccales genomes share a unique composition of genes involved in energy conservation suggesting an original combination of two main energy conservation processes previously described in other methanogens. They also display substantial differences with each other, such as their codon usage, the nature and origin of their CRISPRs systems and the genes possibly involved in particular environmental adaptations. The genome of M. luminyensis encodes several features to thrive in soil and sediment conditions suggesting its larger environmental distribution than GIT. Conversely, "Ca. M. alvus" and "Ca. M. intestinalis" do not present these features and could be more restricted and specialized on GIT. Prediction of the amber codon usage, either as a termination signal of translation or coding for pyrrolysine revealed contrasted patterns among the three genomes and suggests a different handling of the Pyl-encoding capacity. CONCLUSIONS This study represents the first insights into the genomic organization and metabolic traits of the seventh order of methanogens. It suggests contrasted evolutionary history among the three analyzed Methanomassiliicoccales representatives and provides information on conserved characteristics among the overall methanogens and among Thermoplasmata.
Collapse
Affiliation(s)
- Guillaume Borrel
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
- />School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Nicolas Parisot
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
- />CNRS, UMR 6023, Université Blaise Pascal, 63000 Clermont-Ferrand, France
| | - Hugh MB Harris
- />School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Eric Peyretaillade
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - Nadia Gaci
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - William Tottey
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - Olivier Bardot
- />GReD, CNRS, UMR 6293, Inserm, UMR 1103, Clermont Université, Université d’Auvergne 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - Kasie Raymann
- />Département de Microbiologie, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Paris Cedex 15, 75724 France
- />Cellule Pasteur UPMC, Université Pierre et Marie Curie, Paris Cedex 15, 75724 France
| | - Simonetta Gribaldo
- />Département de Microbiologie, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Paris Cedex 15, 75724 France
- />Cellule Pasteur UPMC, Université Pierre et Marie Curie, Paris Cedex 15, 75724 France
| | - Pierre Peyret
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| | - Paul W O’Toole
- />School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Jean-François Brugère
- />EA-4678 CIDAM, Clermont Université, Université d’Auvergne, 28 Place Henri Dunant, BP 10448, 63000 Clermont-Ferrand, France
| |
Collapse
|
7
|
|
8
|
Genetic Confirmation of the Role of Sulfopyruvate Decarboxylase in Coenzyme M Biosynthesis in Methanococcus maripaludis. ARCHAEA 2013; 2013:185250. [PMID: 24151448 PMCID: PMC3787637 DOI: 10.1155/2013/185250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/08/2013] [Indexed: 12/04/2022]
Abstract
Coenzyme M is an essential coenzyme for methanogenesis. The proposed biosynthetic pathway consists of five steps, of which the fourth step is catalyzed by sulfopyruvate decarboxylase (ComDE). Disruption of the gene comE by transposon mutagenesis resulted in a partial coenzyme M auxotroph, which grew poorly in the absence of coenzyme M and retained less than 3% of the wild type level of coenzyme M biosynthesis. Upon coenzyme M addition, normal growth of the mutant was restored. Moreover, complementation of the mutation with the wild type comE gene in trans restored full growth in the absence of coenzyme M. These results confirm that ComE plays an important role in coenzyme M biosynthesis. The inability to yield a complete CoM auxotroph suggests that either the transposon insertion failed to completely inactivate the gene or M. maripaludis possesses a promiscuous activity that partially complemented the mutation.
Collapse
|
9
|
|
10
|
Broberg CA, Clark DD. Shotgun proteomics of Xanthobacter autotrophicus Py2 reveals proteins specific to growth on propylene. Arch Microbiol 2010; 192:945-57. [DOI: 10.1007/s00203-010-0623-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 08/13/2010] [Indexed: 11/28/2022]
|
11
|
Convergent evolution of coenzyme M biosynthesis in the Methanosarcinales: cysteate synthase evolved from an ancestral threonine synthase. Biochem J 2009; 424:467-78. [PMID: 19761441 DOI: 10.1042/bj20090999] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The euryarchaeon Methanosarcina acetivorans has no homologues of the first three enzymes that produce the essential methanogenic coenzyme M (2-mercaptoethanesulfonate) in Methanocaldococcus jannaschii. A single M. acetivorans gene was heterologously expressed to produce a functional sulfopyruvate decarboxylase protein, the fourth canonical enzyme in this biosynthetic pathway. An adjacent gene, at locus MA3297, encodes one of the organism's two threonine synthase homologues. When both paralogues from this organism were expressed in an Escherichia coli threonine synthase mutant, the MA1610 gene complemented the thrC mutation, whereas the MA3297 gene did not. Both PLP (pyridoxal 5'-phosphate)-dependent proteins were heterologously expressed and purified, but only the MA1610 protein catalysed the canonical threonine synthase reaction. The MA3297 protein specifically catalysed a new beta-replacement reaction that converted L-phosphoserine and sulfite into L-cysteate and inorganic phosphate. This oxygen-independent mode of sulfonate biosynthesis exploits the facile nucleophilic addition of sulfite to an alpha,beta-unsaturated intermediate (PLP-bound dehydroalanine). An amino acid sequence comparison indicates that cysteate synthase evolved from an ancestral threonine synthase through gene duplication, and the remodelling of active site loop regions by amino acid insertion and substitutions. The cysteate product can be converted into sulfopyruvate by an aspartate aminotransferase enzyme, establishing a new convergent pathway for coenzyme M biosynthesis that appears to function in members of the orders Methanosarcinales and Methanomicrobiales. These differences in coenzyme M biosynthesis afford the opportunity to develop methanogen inhibitors that discriminate between the classes of methanogenic archaea.
Collapse
|
12
|
Abstract
Coenzyme M (2-mercaptoethanesulfonate; CoM) is one of several atypical cofactors discovered in methanogenic archaea which participate in the biological reduction of CO(2) to methane. Elegantly simple, CoM, so named for its role as a methyl carrier in all methanogenic archaea, is the smallest known organic cofactor. It was thought that this cofactor was used exclusively in methanogenesis until it was recently discovered that CoM is a key cofactor in the pathway of propylene metabolism in the gram-negative soil microorganism Xanthobacter autotrophicus Py2. A four-step pathway requiring CoM converts propylene and CO(2) to acetoacetate, which feeds into central metabolism. In this process, CoM is used to activate and convert highly electrophilic epoxypropane, formed from propylene epoxidation, into a nucleophilic species that undergoes carboxylation. The unique properties of CoM provide a chemical handle for orienting compounds for site-specific redox chemistry and stereospecific catalysis. The three-dimensional structures of several of the enzymes in the pathway of propylene metabolism in defined states have been determined, providing significant insights into both the enzyme mechanisms and the role of CoM in this pathway. These studies provide the structural basis for understanding the efficacy of CoM as a handle to direct organic substrate transformations at the active sites of enzymes.
Collapse
|
13
|
Drevland RM, Waheed A, Graham DE. Enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in Methanocaldococcus jannaschii. J Bacteriol 2007; 189:4391-400. [PMID: 17449626 PMCID: PMC1913355 DOI: 10.1128/jb.00166-07] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The archaeon Methanocaldococcus jannaschii uses three different 2-oxoacid elongation pathways, which extend the chain length of precursors in leucine, isoleucine, and coenzyme B biosyntheses. In each of these pathways an aconitase-type hydrolyase catalyzes an hydroxyacid isomerization reaction. The genome sequence of M. jannaschii encodes two homologs of each large and small subunit that forms the hydrolyase, but the genes are not cotranscribed. The genes are more similar to each other than to previously characterized isopropylmalate isomerase or homoaconitase enzyme genes. To identify the functions of these homologs, the four combinations of subunits were heterologously expressed in Escherichia coli, purified, and reconstituted to generate the iron-sulfur center of the holoenzyme. Only the combination of MJ0499 and MJ1277 proteins catalyzed isopropylmalate and citramalate isomerization reactions. This pair also catalyzed hydration half-reactions using citraconate and maleate. Another broad-specificity enzyme, isopropylmalate dehydrogenase (MJ0720), catalyzed the oxidative decarboxylation of beta-isopropylmalate, beta-methylmalate, and d-malate. Combined with these results, phylogenetic analysis suggests that the pyruvate pathway to 2-oxobutyrate (an alternative to threonine dehydratase in isoleucine biosynthesis) evolved several times in bacteria and archaea. The enzymes in the isopropylmalate pathway of leucine biosynthesis facilitated the evolution of 2-oxobutyrate biosynthesis through the introduction of a citramalate synthase, either by gene recruitment or gene duplication and functional divergence.
Collapse
Affiliation(s)
- Randy M Drevland
- Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | | | | |
Collapse
|
14
|
Abstract
As the molecular adapters between codons and amino acids, transfer-RNAs are pivotal molecules of the genetic code. The coding properties of a tRNA molecule do not reside only in its primary sequence. Posttranscriptional nucleoside modifications, particularly in the anticodon loop, can modify cognate codon recognition, affect aminoacylation properties, or stabilize the codon-anticodon wobble base pairing to prevent ribosomal frameshifting. Despite a wealth of biophysical and structural knowledge of the tRNA modifications themselves, their pathways of biosynthesis had been until recently only partially characterized. This discrepancy was mainly due to the lack of obvious phenotypes for tRNA modification-deficient strains and to the difficulty of the biochemical assays used to detect tRNA modifications. However, the availability of hundreds of whole-genome sequences has allowed the identification of many of these missing tRNA-modification genes. This chapter reviews the methods that were used to identify these genes with a special emphasis on the comparative genomic approaches. Methods that link gene and function but do not rely on sequence homology will be detailed, with examples taken from the tRNA modification field.
Collapse
|
15
|
DiDonato M, Krishna SS, Schwarzenbacher R, McMullan D, Agarwalla S, Brittain SM, Miller MD, Abdubek P, Ambing E, Axelrod HL, Canaves JM, Chiu HJ, Deacon AM, Duan L, Elsliger MA, Godzik A, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, Spraggon G, Stevens RC, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of 2-phosphosulfolactate phosphatase (ComB) fromClostridium acetobutylicumat 2.6 Å resolution reveals a new fold with a novel active site. Proteins 2006; 65:771-6. [PMID: 16927339 DOI: 10.1002/prot.20978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
16
|
Helgadóttir S, Rosas-Sandoval G, Söll D, Graham DE. Biosynthesis of phosphoserine in the Methanococcales. J Bacteriol 2006; 189:575-82. [PMID: 17071763 PMCID: PMC1797378 DOI: 10.1128/jb.01269-06] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanococcus maripaludis and Methanocaldococcus jannaschii produce cysteine for protein synthesis using a tRNA-dependent pathway. These methanogens charge tRNA(Cys) with l-phosphoserine, which is also an intermediate in the predicted pathways for serine and cystathionine biosynthesis. To establish the mode of phosphoserine production in Methanococcales, cell extracts of M. maripaludis were shown to have phosphoglycerate dehydrogenase and phosphoserine aminotransferase activities. The heterologously expressed and purified phosphoglycerate dehydrogenase from M. maripaludis had enzymological properties similar to those of its bacterial homologs but was poorly inhibited by serine. While bacterial enzymes are inhibited by micromolar concentrations of serine bound to an allosteric site, the low sensitivity of the archaeal protein to serine is consistent with phosphoserine's position as a branch point in several pathways. A broad-specificity class V aspartate aminotransferase from M. jannaschii converted the phosphohydroxypyruvate product to phosphoserine. This enzyme catalyzed the transamination of aspartate, glutamate, phosphoserine, alanine, and cysteate. The M. maripaludis homolog complemented a serC mutation in the Escherichia coli phosphoserine aminotransferase. All methanogenic archaea apparently share this pathway, providing sufficient phosphoserine for the tRNA-dependent cysteine biosynthetic pathway.
Collapse
Affiliation(s)
- Sunna Helgadóttir
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | | | | | | |
Collapse
|
17
|
Karandashova IV, Semina ME, Muronets EM, Elanskaya IV. Expression of drgA gene encoding NAD(P)H:quinone-oxidoreductase in the cyanobacterium Synechocystis sp. PCC 6803. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406080047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
18
|
Tsoka S, Simon D, Ouzounis CA. Automated metabolic reconstruction for Methanococcus jannaschii. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2005; 1:223-9. [PMID: 15810431 PMCID: PMC2685575 DOI: 10.1155/2004/324925] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We present the computational prediction and synthesis of the metabolic pathways in Methanococcus jannaschii from its genomic sequence using the PathoLogic software. Metabolic reconstruction is based on a reference knowledge base of metabolic pathways and is performed with minimal manual intervention. We predict the existence of 609 metabolic reactions that are assembled in 113 metabolic pathways and an additional 17 super-pathways consisting of one or more component pathways. These assignments represent significantly improved enzyme and pathway predictions compared with previous metabolic reconstructions, and some key metabolic reactions, previously missing, have been identified. Our results, in the form of enzymatic assignments and metabolic pathway predictions, form a database (MJCyc) that is accessible over the World Wide Web for further dissemination among members of the scientific community.
Collapse
Affiliation(s)
- Sophia Tsoka
- Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.
| | | | | |
Collapse
|
19
|
Hand CE, Honek JF. Biological chemistry of naturally occurring thiols of microbial and marine origin. JOURNAL OF NATURAL PRODUCTS 2005; 68:293-308. [PMID: 15730267 DOI: 10.1021/np049685x] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The presence of thiols in living systems is critical for the maintenance of cellular redox potentials and protein thiol-disulfide ratios, as well as for the protection of cells from reactive oxygen species. In addition to the well-studied tripeptide glutathione (gamma-Glu-Cys-Gly), a number of compounds have been identified that contribute to these essential cellular roles. This review provides a survey of the chemistry and biochemistry of several critically important and naturally occurring intracellular thiols such as coenzyme M, trypanothione, mycothiol, ergothioneine, and the ovothiols. Coenzyme M is a key thiol required for methane production in methogenic bacteria. Trypanothione and mycothiol are very important to the biochemistry of a number of human pathogens, and the enzymes utilizing these thiols have been recognized as important novel drug targets. Ergothioneine, although synthesized by fungi and the Actinomycetales bacteria, is present at significant physiological levels in humans and may contribute to single electron redox reactions in cells. The ovothiols appear to function as important modulators of reactive oxygen toxicity and appear to serve as small molecule mimics of glutathione peroxidase, a key enzyme in the detoxification of reactive oxygen species.
Collapse
Affiliation(s)
- Christine E Hand
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | | |
Collapse
|
20
|
|
21
|
Abstract
In the genomics era, the interactions between proteins are at the center of attention. Genomic-context methods used to predict these interactions have been put on a quantitative basis, revealing that they are at least on an equal footing with genomics experimental data. A survey of experimentally confirmed predictions proves the applicability of these methods, and new concepts to predict protein interactions in eukaryotes have been described. Finally, the interaction networks that can be obtained by combining the predicted pair-wise interactions have enough internal structure to detect higher levels of organization, such as 'functional modules'.
Collapse
Affiliation(s)
- Martijn A Huynen
- Nijmegen Center for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands.
| | | | | | | |
Collapse
|
22
|
Affiliation(s)
- William C Nierman
- Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
| | | |
Collapse
|
23
|
Graham DE, Xu H, White RH. Identification of coenzyme M biosynthetic phosphosulfolactate synthase: a new family of sulfonate-biosynthesizing enzymes. J Biol Chem 2002; 277:13421-9. [PMID: 11830598 DOI: 10.1074/jbc.m201011200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hyperthermophilic euryarchaeon Methanococcus jannaschii uses coenzyme M (2-mercaptoethanesulfonic acid) as the terminal methyl carrier in methanogenesis. We describe an enzyme from that organism, (2R)-phospho-3-sulfolactate synthase (ComA), that catalyzes the first step in coenzyme M biosynthesis. ComA catalyzed the stereospecific Michael addition of sulfite to phosphoenolpyruvate over a broad range of temperature and pH conditions. Substrate and product analogs moderately inhibited activity. This enzyme has no significant sequence similarity to previously characterized enzymes; however, its Mg(2+)-dependent enzyme reaction mechanism may be analogous to one proposed for enolase. A diverse group of microbes and plants have homologs of ComA that could have been recruited for sulfolactate or sulfolipid biosyntheses.
Collapse
Affiliation(s)
- David E Graham
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0308, USA
| | | | | |
Collapse
|