DOCSLIB.ORG

Functional Context, Biosynthesis, and Genetic Encoding of Pyrrolysine Marsha a Gaston1, Ruisheng Jiang2 and Joseph a Krzycki1,2

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Functional Context, Biosynthesis, and Genetic Encoding of Pyrrolysine Marsha a Gaston1, Ruisheng Jiang2 and Joseph a Krzycki1,2 COMICR-868; NO. OF PAGES 8 Available online at www.sciencedirect.com Functional context, biosynthesis, and genetic encoding of pyrrolysine Marsha A Gaston1, Ruisheng Jiang2 and Joseph A Krzycki1,2 In Methanosarcina spp., amber codons in methylamine methylate a cognate corrinoid protein (MttC, MtbC, or methyltransferase genes are translated as the 22nd amino acid, MtmC) in the Co(I) state. Adventitious oxidation of the pyrrolysine. The responsible pyl genes plus amber-codon corrinoid proteins to Co(II) can inactivate the methyltrans- containing methyltransferase genes have been identified in four ferase reactions, but the iron-sulfur protein RamA can archaeal and five bacterial genera, including one human activate the corrinoid proteins via ATP dependent pathogen. In Escherichia coli, the recombinant pylBCD gene reduction [7]. The methyl-Co(III) corrinoid proteins products biosynthesize pyrrolysine from two molecules of are substrates of MtbA which methylates coenzyme M lysine and the pylTS gene products direct pyrrolysine (CoM) [8,9]. From here, methyl groups can be converted to incorporation into protein. In the proposed biosynthetic carbon dioxide, methane, and cell carbon. pathway, PylB forms methylornithine from lysine, which is joined to another lysine by PylC, and oxidized to pyrrolysine by MttB, MtbB, or MtmB have no significant sequence PylD. Structures of the catalytic domain of pyrrolysyl-tRNA similarity, but each of their genes contains a single in- synthetase (archaeal PylS or bacterial PylSc) revealed binding frame amber codon [10,11] that is translated [12,13]. The sites for tRNAPyl and pyrrolysine. PylS and tRNAPyl are now crystal structure of MtmB revealed pyrrolysine as the being exploited as an orthogonal pair in recombinant systems UAG-encoded residue [3,14]. Mass spectral studies for introduction of useful modified amino acids into proteins. demonstrated that the UAG-encoded residues of MttB Addresses and MtbB are also pyrrolysine [13]. Pyrrolysine was 1 Department of Microbiology, 484 West 12th Avenue, The Ohio State observed in the crystal structure to bind ammonia at University, Columbus, OH 43210, United States the carbon of the imine bond [3,14], and it is hypothesized 2 The Ohio State University Biochemistry Program, 484 West 12th that a pyrrolysine–methylammonium adduct serves to Avenue, The Ohio State University, Columbus, OH 43210, United States activate and orient methylamines as substrates for nucleo- Corresponding author: Krzycki, Joseph A ([email protected]) philic attack by the Co(I) corrinoid protein (Figure 1) [3,15]. Current Opinion in Microbiology 2011, 14:1–8 Pyrrolysine is synthesized and incorporated into the meth- This review comes from a themed issue on ylamine methyltransferases through the combined actions Archaea of the products of the pyl genes (Figure 1). The pylT gene Edited by John Reeve and Christa Schleper encodes tRNAPyl whose CUA anticodon allows for amber codon translation [2,16]. The pylS gene produces the pyrrolysyl-tRNA synthetase that charges tRNAPyl directly 1369-5274/$ – see front matter with pyrrolysine [17,18]. The synthesis of pyrrolysine is # 2011 Elsevier Ltd. All rights reserved. carried out by the pylBCD gene products [19]. DOI 10.1016/j.mib.2011.04.001 Incorporation of pyrrolysine into protein under the direction of amber codons does not require specific signals in the gene, as in-frame amber codons inserted Introduction into the Escherichia coli uidA gene for b-glucuronidase are Methanogenesis is a process unique to the Archaea. Befit- translated as pyrrolysine at 20–30% efficiency in Metha- tingly, many unusual enzymes, cofactors, and metabolites nosarcina acetivorans [20,21 ]. Translation of UAG as were first encountered in methanogens and only later in pyrrolysine even in foreign genes with an introduced bacteria [1]. One such find is pyrrolysine, the 22nd amino amber codon suggests this level of translation occurs by a acid to be encountered in the natural genetic code [2,3]. mechanism analogous to that underlying amber suppres- sion, with tRNAPyl acting as a suppressor tRNA. On the In Archaea, the pyrrolysyl residue is known to occur only in other hand, UAG translation in the methanogen with the family Methanosarcinaceae. Unlike most other methano- mtmB1 transcripts appears much more efficient, with gens, members of this group can use methylamines as little UAG-termination product detectable. Substitution precursors to methane. Metabolism of trimethylamine, of sequence immediately downstream of the UAG codon dimethylamine, or monomethylamine is respectively dramatically increases the UAG-termination product, initiated by the pyrrolysine-containing proteins MttB, but with still a relatively high level of UAG translation MtbB, or MtmB (Figure 1)[4–6]. These proteins each as pyrrolysine. While the deleted region may act as a www.sciencedirect.com Current Opinion in Microbiology 2011, 14:1–8 Please cite this article in press as: Gaston MA, et al. Functional context, biosynthesis, and genetic encoding of pyrrolysine, Curr Opin Microbiol (2011), doi:10.1016/j.mib.2011.04.001 COMICR-868; NO. OF PAGES 8 2 Archaea Figure 1 (2R,3R)-3-methylornithinyl- (2R,3R)-3-methylglutamyl- Pyrrolysine (Pyl) (2R,3R)-3-methylornithine N6-lysine 5-semialdehyde-N6-lysine (Z) NH NH NH 2 2 2 (R) N H2N (R) O H2N (R) O O (R) O (R) (R) (R) (R) O PylB OH H2N HN HN HN SAM H O PylD 2 ATP PylC NH H2O 3 (S) NH (S) NH 2 [H] (S) NH (S) 2 2 2 NH2 HO HO HO HO O O O O Lysine (x 2) PylT Pyl mtmB, mtbB, mttB transcripts (tRNAPyl) Translation of UAG as Pyl PylS R + 1 NH CH3 2 CH H N 3 R1 .. R2 N Co (III) HSCoM R2 MtmB MtbB MttB MtmC MtbC MttC R =H R =H R =CH MtbA 1 1 1 3 (MtmB) (MtbB) (MttB) CH4 R2=H R2=CH3 R2=CH3 CH3 R2 R1 N+ CH SCoM CO Co (I) 3 2 H N ATP RamA Cell C - e- e Co (II) Current Opinion in Microbiology Schematic of pyrrolysine and methylamine metabolism in Methanosarcina spp. Pyrrolysine is made from two molecules of lysine. In the proposed pathway, PylB converts one lysine into a methylated D-ornithine derivative, which is then ligated to another lysine by PylC. The resultant dipeptide is oxidized by PylD, which results in spontaneous elimination of water and formation of pyrrolysine. Pyrrolysine is then ligated to tRNAPyl by PylS. The pyrrolysyl-tRNAPyl is carried to the ribosome by the usual elongation factor for cotranslational incorporation into one of the three methylamine methyltransferases, MtmB, MtbB, or MttB. Below each methyltransferase is indicated its particular methylamine substrate. Pyrrolysine in the catalytic site is hypothesized to form an adduct with that methylamine which orients and activates it for methyl group transfer to the Co(I) form of the corrinoid cofactor bound to either MtmC, MtbC, or MttC. Each corrinoid protein interacts preferentially with the methyltransferase indicated below it. Adventitious oxidation of the corrinoid protein can result in inactivation, and a single protein, RamA, can return the corrinoid protein to the Co(I) state. All three methylated corrinoid proteins can serve as substrates for MtbA, which methylates the thiol of CoM (HSCoM). Methyl-CoM can then serve to directly generate methane, or to enter pathways leading to carbon assimilation and carbon dioxide production. Further details are provided in the text. sequence enhancing translation over termination with sequencing has now expanded the count to six bacterial mtmB1 transcripts, previous suggestions from several and six archaeal species belonging to nine genera laboratories of an obligate pyrrolysine insertion element (Figure 2). In the archaea, pyl genes are still limited to or tRNAPyl specific translation factors have not been members of the Methanosarcinaceae, but now also include borne out [20–24]. psychrotrophic methanogen Methanococcoides burtonii, and two halophilic methanogens, Methanohalophilus mahii and Sequenced genomes with pyl genes Methanohalobium evestigatum. The pyl genes are also found At the time of the discovery of pyrrolysine, only Metha- in selected species of the bacterial groups Clostridia or the nosarcina spp. and the bacterium Desulfitobacterium haf- Deltaproteobacteria. The latter group includes symbionts niense were known to possess pyl genes [2]. Recent of multicellular organisms, such as a gut inhabitant of a Current Opinion in Microbiology 2011, 14:1–8 www.sciencedirect.com Please cite this article in press as: Gaston MA, et al. Functional context, biosynthesis, and genetic encoding of pyrrolysine, Curr Opin Microbiol (2011), doi:10.1016/j.mib.2011.04.001 COMICR-868; NO. OF PAGES 8 Functional context, biosynthesis, and genetic encoding of pyrrolysine Gaston, Jiang and Krzycki 3 marine worm identified in a metagenomic study [25,26]. [32]. In bacteria, N-terminal and C-terminal domains of Most recently, pyl genes were annotated in the genome of archaeal PylS are respectively represented by two inde- the human intestinal bacteria, Bilophila wadsworthia pendent proteins, PylSn and PylSc (Figure 2)[2,32]. (Figure 2). The unannotated pylT gene was identified by the authors some distance from the other pyl genes Crystal structures of the C-terminal domain of archaeal (Figure 2, Figure S1). This organism has been a common PylS and bacterial PylSc have revealed the catalytic site isolate in cases of gangrenous appendicitis and abscesses that accommodates pyrrolysine and ATP [30,31,33, in a variety of bodily locations [27], and represents the 34,35]. The pyrrolysine ring is accommodated by a first known human symbiont, and pathogen, to have hydrophobic pocket closed by a mobile loop bearing a pyrrolysine genes. tyrosine which may H-bond the imine nitrogen of pyrro- lysine [30], and/or provide stability to the formed pyrro- While amber codons have been identified in Thg1 and lysyl-adenylate before tRNA binding [33]. While transposase genes of one or two Methanosarcina spp., these pyrrolysine has the most favorable kinetics for amino acid are likely to be mutations stable in the context of tRNAPyl activation, analogs having an oxygen atom replacing the and PylS, as homologs of these genes without amber imine nitrogen are favored over those with carbon, codons exist in other Methanosarcinaceae [21,28,29].
Load more

Recommended publications
  • Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea
    Hindawi Publishing Corporation Archaea Volume 2010, Article ID 453642, 14 pages doi:10.1155/2010/453642 Review Article Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea Michael Rother1 and Joseph A. Krzycki2 1 Institut fur¨ Molekulare Biowissenschaften, Molekulare Mikrobiologie & Bioenergetik, Johann Wolfgang Goethe-Universitat,¨ Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany 2 Department of Microbiology, The Ohio State University, 376 Biological Sciences Building 484 West 12th Avenue Columbus, OH 43210-1292, USA Correspondence should be addressed to Michael Rother, [email protected] andJosephA.Krzycki,[email protected] Received 15 June 2010; Accepted 13 July 2010 Academic Editor: Jerry Eichler Copyright © 2010 M. Rother and J. A. Krzycki. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Methanogenic archaea are a group of strictly anaerobic microorganisms characterized by their strict dependence on the process of methanogenesis for energy conservation. Among the archaea, they are also the only known group synthesizing proteins containing selenocysteine or pyrrolysine. All but one of the known archaeal pyrrolysine-containing and all but two of the confirmed archaeal selenocysteine-containing protein are involved in methanogenesis. Synthesis of these proteins proceeds through suppression of translational stop codons but otherwise the two systems are fundamentally different. This paper highlights these differences and summarizes the recent developments in selenocysteine- and pyrrolysine-related research on archaea and aims to put this knowledge into the context of their unique energy metabolism. 1. Introduction found to correspond to pyrrolysine in the crystal structure [9, 10] and have its own tRNA [11].
    [Show full text]
  • The Vertical Distribution of Sediment Archaeal Community in the (Black Bloom) Disturbing Zhushan Bay of Lake Taihu
    Hindawi Publishing Corporation Archaea Volume 2016, Article ID 8232135, 8 pages http://dx.doi.org/10.1155/2016/8232135 Research Article The Vertical Distribution of Sediment Archaeal Community in the (Black Bloom) Disturbing Zhushan Bay of Lake Taihu Xianfang Fan1,2 and Peng Xing1 1 State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing 210008, China 2State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China Correspondence should be addressed to Peng Xing; [email protected] Received 20 August 2015; Revised 27 November 2015; Accepted 20 December 2015 Academic Editor: William B. Whitman Copyright © 2016 X. Fan and P. Xing. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Using the Illumina sequencing technology, we investigated the vertical distribution of archaeal community in the sediment of Zhushan Bay of Lake Taihu, where the black bloom frequently occurred in summer. Overall, the Miscellaneous Crenarchaeotal Group (MCG), Deep Sea Hydrothermal Vent Group 6 (DHVEG-6), and Methanobacterium dominated the archaeal community. However, we observed significant difference in composition of archaeal community among different depths of the sediment. DHVEG-6 dominated in the surface layer (0–3 cm) sediment. Methanobacterium was the dominating archaeal taxa in the L2 (3– 6 cm) and L3 (6–10) sediment. MCG was most abundant in the L4 (10–15 cm) and L5 (15–20 cm) sediment. Besides, DHVEG-6 was significantly affected by the concentration of total phosphorus ).(TP And loss on ignition (LOI) was an important environmental factor for Methanobacterium.
    [Show full text]
  • Amino Acid Recognition by Aminoacyl-Trna Synthetases
    www.nature.com/scientificreports OPEN The structural basis of the genetic code: amino acid recognition by aminoacyl‑tRNA synthetases Florian Kaiser1,2,4*, Sarah Krautwurst3,4, Sebastian Salentin1, V. Joachim Haupt1,2, Christoph Leberecht3, Sebastian Bittrich3, Dirk Labudde3 & Michael Schroeder1 Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defnes the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process. We extensively characterize how these enzymes distinguish all natural amino acids based on the computational analysis of crystallographic structure data. The results of this meta-analysis show that the correct read-out of genetic information is a delicate interplay between the composition of the binding site, non-covalent interactions, error correction mechanisms, and steric efects. One of the most profound open questions in biology is how the genetic code was established. While proteins are encoded by nucleic acid blueprints, decoding this information in turn requires proteins. Te emergence of this self-referencing system poses a chicken-or-egg dilemma and its origin is still heavily debated 1,2. Aminoacyl-tRNA synthetases (aaRSs) implement the correct assignment of amino acids to their codons and are thus inherently connected to the emergence of genetic coding. Tese enzymes link tRNA molecules with their amino acid cargo and are consequently vital for protein biosynthesis. Beside the correct recognition of tRNA features3, highly specifc non-covalent interactions in the binding sites of aaRSs are required to correctly detect the designated amino acid4–7 and to prevent errors in biosynthesis5,8.
    [Show full text]
  • THE MASS of L-PYRROLYSINE in METHYLAMINE METHYLTRANSFERASES and the ROLE of ITS IMINE BOND in CATALYSIS DISSERTATION Presented I
    THE MASS OF L-PYRROLYSINE IN METHYLAMINE METHYLTRANSFERASES AND THE ROLE OF ITS IMINE BOND IN CATALYSIS DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in the Graduate School of The Ohio State University by Jitesh Anthony Aloysius Soares, M.S. The Ohio State University 2008 Dissertation Committee: Dr. Joseph A. Krzycki, Advisor Approved by Dr. Charles J. Daniels Dr. Mark Morrison ______________________ Dr. F. Robert Tabita Advisor Graduate Program in Microbiology ABSTRACT Methanosarcina barkeri is an archaeon capable of producing methane from methylamines. Methylamine methyltransferases initiate methanogenesis from methylamines by transferring methyl groups to a cognate corrinoid protein. Each gene encoding a methylamine methyltransferase has been shown to contain a single in-frame amber codon. Further studies have shown that in the monomethylamine methyltransferase, mtmB , the amber codon encodes a novel amino acid, L-pyrrolysine. X-ray crystal structures of MtmB have shown that the structure of this amino acid is a lysine residue with the epsilon-nitrogen in amide linkage to a (4R, 5R)-4-substituted pyrrolyine-5-carboxylate ring. However, these structures did not allow an assignment of the pyrroline ring C4 substituent as a methyl or amine group. In this thesis (Chapter 2) mass spectrometry of chymotryptic digests of methylamine methyltransferases is employed to show that pyrrolysine in present in all three types of methylamine methyltransferase at the position corresponding to the amber codon in their respective genes. The mass of this amber-encoded residue was observed to coincide with the predicted mass of pyrrolysine with a methyl- group at the C4 position.
    [Show full text]
  • Direct Charging of Trnacua with Pyrrolysine in Vitro and in Vivo
    letters to nature .............................................................. gene product (see Supplementary Fig. S1). The tRNA pool extracted from Methanosarcina acetivorans or tRNACUA transcribed in vitro Direct charging of tRNACUA with was used in charging experiments. Charged and uncharged tRNA species were separated by electrophoresis in a denaturing acid-urea pyrrolysine in vitro and in vivo 10,11 polyacrylamide gel and tRNACUA was specifically detected by northern blotting with an oligonucleotide probe. The oligonucleo- Sherry K. Blight1*, Ross C. Larue1*, Anirban Mahapatra1*, tide complementary to tRNA could hybridize to a tRNA in the David G. Longstaff1, Edward Chang1, Gang Zhao2†, Patrick T. Kang4, CUA Kari B. Green-Church5, Michael K. Chan2,3,4 & Joseph A. Krzycki1,4 pool of tRNAs isolated from wild-type M. acetivorans but not to the tRNA pool from a pylT deletion mutant of M. acetivorans (A.M., 1Department of Microbiology, 484 West 12th Avenue, 2Department of Chemistry, A. Patel, J. Soares, R.L. and J.A.K., unpublished observations). 3 100 West 18th Avenue, Department of Biochemistry, 484 West 12th Avenue, Both tRNACUA and aminoacyl-tRNACUA were detectable in the The Ohio State University, Columbus, Ohio 43210, USA isolated cellular tRNA pool (Fig. 1). Alkaline hydrolysis deacylated 4Ohio State University Biochemistry Program, 484 West 12th Avenue, The Ohio the cellular charged species, but subsequent incubation with pyrro- State University, Columbus, Ohio 43210, USA lysine, ATP and PylS-His6 resulted in maximal conversion of 50% of 5CCIC/Mass Spectrometry and Proteomics Facility, The Ohio State University, deacylated tRNACUA to a species that migrated with the same 116 W 19th Ave, Columbus, Ohio 43210, USA electrophoretic mobility as the aminoacyl-tRNACUA present in the * These authors contributed equally to this work.
    [Show full text]
  • Site-Specific Protein Modifications Through Pyrroline-Carboxy-Lysine Residues
    Site-specific protein modifications through pyrroline-carboxy-lysine residues Weijia Ou1, Tetsuo Uno1, Hsien-Po Chiu, Jan Grünewald, Susan E. Cellitti, Tiffany Crossgrove, Xueshi Hao, Qian Fan, Lisa L. Quinn, Paula Patterson, Linda Okach, David H. Jones, Scott A. Lesley, Ansgar Brock, and Bernhard H. Geierstanger2 Genomics Institute of the Novartis Research Foundation, 10675 John-Jay-Hopkins Drive, San Diego, CA 92121-1125 Edited* by Peter G. Schultz, The Scripps Research Institute, La Jolla, CA, and approved May 11, 2011 (received for review April 4, 2011) Pyrroline-carboxy-lysine (Pcl) is a demethylated form of pyrrolysine acids will face similar hurdles to achieve site-specificity without that is generated by the pyrrolysine biosynthetic enzymes when deleterious effects to the protein of interest. the growth media is supplemented with D-ornithine. Pcl is readily The most elegant way to generate homogenously, site-specifi- incorporated by the unmodified pyrrolysyl-tRNA/tRNA synthetase cally modified proteins is the in vivo incorporation of unnatural pair into proteins expressed in Escherichia coli and in mammalian amino acids (7–9). Over 70 unnatural amino acids featuring a cells. Here, we describe a broadly applicable conjugation chemistry wide array of functionalities can be incorporated at TAG codons that is specific for Pcl and orthogonal to all other reactive groups using specific tRNA/tRNA synthetase pairs engineered through on proteins. The reaction of Pcl with 2-amino-benzaldehyde or an in vivo selection process to be orthogonal to the cellular 2-amino-acetophenone reagents proceeds to near completion at machinery of the host cells. A set of reactive unnatural amino neutral pH with high efficiency.
    [Show full text]
  • Characteristics and Metabolic Patterns of Soil Methanogenic Archaea Communities in the High Latitude Natural Wetlands of China
    Characteristics and Metabolic Patterns of Soil Methanogenic Archaea Communities in the High Latitude Natural Wetlands of China Di Wu Northeast Forestry University Caihong Zhao Northeast Forestry University Hui Bai Forestry Science Research Institute of Heilongjiang Province Fujuan Feng Northeast Forestry University Xin Sui Heilongjiang University Guangyu Sun ( [email protected] ) Northeast Forestry University Research article Keywords: Wetlands, Methanogens, Community diversity, Indicator species, Methanogenic metabolic patterns Posted Date: August 12th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-54821/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/18 Abstract Background: Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. Result: The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably inuenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla – Larix gmelinii wetland was relatively different from the structure of the other two wetland types.
    [Show full text]
  • A Three-Component Microbial Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic Glycine Betaine Degradation with Methanogenesis
    Microorganisms 2015, 3, 500-517; doi:10.3390/microorganisms3030500 OPEN ACCESS microorganisms ISSN 2076-2607 www.mdpi.com/journal/microorganisms Article A Three-Component Microbial Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic Glycine Betaine Degradation with Methanogenesis Violetta La Cono 1, Erika Arcadi 1, Gina La Spada 1, Davide Barreca 2, Giuseppina Laganà 2, Ersilia Bellocco 2, Maurizio Catalfamo 1, Francesco Smedile 1, Enzo Messina 1, Laura Giuliano 1,3 and Michail M. Yakimov 1,* 1 Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina 98122, Italy; E-Mails: [email protected] (V.L.C.); [email protected] (E.A.); [email protected] (G.L.S.); [email protected] (M.C.); [email protected] (F.S.); [email protected] (E.M.); [email protected] (L.G.) 2 Department of Organic and Biological Chemistry, University of Messina, Salita Sperone 31, Villaggio S. Agata, Messina 98166, Italy; E-Mails: [email protected] (D.B.); [email protected] (G.L.); [email protected] (E.B.) 3 Mediterranean Science Commission (CIESM), 16 bd de Suisse, MC 98000, Monaco * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +39-090-6015-437. Academic Editors: Ricardo Amils and Elena González Toril Received: 1 July 2015 / Accepted: 1 September 2015 / Published: 9 September 2015 Abstract: Microbial communities inhabiting the deep-sea salt-saturated anoxic lakes of the Eastern Mediterranean operate under harsh physical-chemical conditions that are incompatible with the lifestyle of common marine microorganisms.
    [Show full text]
  • Hydrogenases of Methanogens
    ANRV413-BI79-18 ARI 27 April 2010 21:0 Hydrogenases from Methanogenic Archaea, Nickel, a Novel Cofactor, and H2 Storage Rudolf K. Thauer, Anne-Kristin Kaster, Meike Goenrich, Michael Schick, Takeshi Hiromoto, and Seigo Shima Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany; email: [email protected] Annu. Rev. Biochem. 2010. 79:507–36 Key Words First published online as a Review in Advance on H2 activation, energy-converting hydrogenase, complex I of the March 17, 2010 respiratory chain, chemiosmotic coupling, electron bifurcation, The Annual Review of Biochemistry is online at reversed electron transfer biochem.annualreviews.org This article’s doi: Abstract 10.1146/annurev.biochem.030508.152103 Most methanogenic archaea reduce CO2 with H2 to CH4. For the Copyright c 2010 by Annual Reviews. activation of H2, they use different [NiFe]-hydrogenases, namely All rights reserved energy-converting [NiFe]-hydrogenases, heterodisulfide reductase- 0066-4154/10/0707-0507$20.00 associated [NiFe]-hydrogenase or methanophenazine-reducing by University of Texas - Austin on 06/10/13. For personal use only. [NiFe]-hydrogenase, and F420-reducing [NiFe]-hydrogenase. The energy-converting [NiFe]-hydrogenases are phylogenetically related Annu. Rev. Biochem. 2010.79:507-536. Downloaded from www.annualreviews.org to complex I of the respiratory chain. Under conditions of nickel limitation, some methanogens synthesize a nickel-independent [Fe]- hydrogenase (instead of F420-reducing [NiFe]-hydrogenase) and by that reduce their nickel requirement. The [Fe]-hydrogenase harbors a unique iron-guanylylpyridinol cofactor (FeGP cofactor), in which a low-spin iron is ligated by two CO, one C(O)CH2-, one S-CH2-, and a sp2-hybridized pyridinol nitrogen.
    [Show full text]
  • Translation of the Amber Codon in Methylamine Methyltransferase Genes of a Methanogenic Archaeon
    TRANSLATION OF THE AMBER CODON IN METHYLAMINE METHYLTRANSFERASE GENES OF A METHANOGENIC ARCHAEON DISSERTATION Presented in Partial Fulfillment of the Requirements for The Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Gayathri Srinivasan, M. S. * * * * * The Ohio State University 2003 Dissertation Committee: Dr. Joseph A. Krzycki, Advisor Approved by Dr. Charles J. Daniels Dr. Tina M. Henkin ________________________ (Advisor) Dr. John N. Reeve Department of Microbiology ABSTRACT Members of the Methanosarcinaceae family can in addition to hydrogen/carbon dioxide utilize several methylated compounds and convert them to methane. Methanogenesis from methylamines involves methylamine specific methyltransferases that transfer the methyl group from the methylamines to a corrinoid protein. The methylamine specific methyltransferase genes contain a single in-frame amber codon that is not read as a translational stop. The residue encoded by the amber codon, has been found to be a novel amino acid, pyrrolysine in MtmB. Multiple copies of monomethylamine methyltransferase genes (mtmB) containing a single amber codon within their open reading frames, along with the genes encoding their cognate corrinoid proteins (mtmC), exist within the genomes of the members of the Methanosarcinaceae family. The two copies of mtmCB genes from M. barkeri MS are differentially transcribed. Editing of the mtmB2 transcript was not detected suggesting a mechanism of amber codon readthrough occurring in the organism. Similar to selenocysteine incorporation at UGA codons, the Methanosarcinaceae also appear to have a unique mechanism for amber codon readthrough. An amber decoding tRNA gene, pylT, along with its cognate lysyl tRNA synthetase, pylS, are found near the MMA methyltransferase gene cluster.
    [Show full text]
  • Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules
    Brigham Young University BYU ScholarsArchive Theses and Dissertations 2014-07-01 Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Ryan M. Taylor Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Biochemistry Commons, and the Chemistry Commons BYU ScholarsArchive Citation Taylor, Ryan M., "Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules" (2014). Theses and Dissertations. 5585. https://scholarsarchive.byu.edu/etd/5585 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Ryan M. Taylor A dissertation submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Doctor of Philosophy John T. Prince, Chair Mark Clement Steven W. Graves Barry M. Willardson Dixon J. Woodbury Department of Chemistry and Biochemistry Brigham Young University July 2014 Copyright © 2014 Ryan M. Taylor All Rights Reserved ABSTRACT Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Ryan M. Taylor Department of Chemistry and Biochemistry, BYU Doctor of Philosophy Biological research has benefitted greatly from the advent of omic methods. For many biomolecules, mass spectrometry (MS) methods are most widely employed due to the sensitivity which allows low quantities of sample and the speed which allows analysis of complex samples. Improvements in instrument and sample preparation techniques create opportunities for large scale experimentation.
    [Show full text]
  • A Systematic Approach Re-Analyzing the Effects of Temperature
    www.nature.com/scientificreports OPEN A systematic approach re-analyzing the efects of temperature disturbance on the microbial Received: 12 September 2018 Accepted: 12 April 2019 community of mesophilic anaerobic Published: xx xx xxxx digestion Grace Tzun-Wen Shaw , Chieh-Yin Weng, Cheng-Yu Chen , Francis Cheng-Hsuan Weng & Daryi Wang Microbial communities are key drivers of ecosystem processes, but their behavior in disturbed environments is difcult to measure. How microbial community composition and function respond disturbances is a common challenge in biomedical, environmental, agricultural, and bioenergy research. A novel way to solve this problem is to use a systems-level perspective and describe microbial communities as networks. Based on a mesophilic anaerobic digestion system of swine manure as a tool, we propose a simple framework to investigate changes in microbial communities via compositions, metabolic pathways, genomic properties and interspecies relationships in response to a long-term temperature disturbance. After temperature disturbance, microbial communities tend towards a competitive interaction network with higher GC content and larger genome size. Based on microbial interaction networks, communities responded to the disturbance by showing a transition from acetotrophic (Methanotrichaceae and Methanosarcinaceae) to methylotrophic methanogens (Methanomassiliicoccaceae and Methanobacteriaceae) and a fuctuation in rare biosphere taxa. To conclude, this study may be important for exploring the dynamic relationships between disturbance and microbial communities as a whole, as well as for providing researchers with a better understanding of how changes in microbial communities relate to ecological processes. Environmental disturbances are important factors in shaping the structure of plant, animal or microbial pop- ulations. In the past few decades, remarkable progress has been made towards understanding how disturbance afects microbial composition, biodiversity loss and ecological processes1–5.
    [Show full text]