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Translation of the Amber Codon in Methylamine Methyltransferase Genes of a Methanogenic Archaeon

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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. The pylT and pylS genes are co- transcribed. Homologs of pylS and pylT are found in a Gram-positive bacterium that also ii contains a trimethylamine methyltransferase gene homolog with a single in-frame amber codon in its open reading frame. Two additional lysyl-tRNA synthetases, LysK and LysS, occur in M. barkeri. Comparison of tRNA substrate specificity of the three lysyl-tRNA synthetases showed that LysK and LysS have slower rate of charging of the in vitro transcript of pylT (the gene encoding the amber decoding tRNA) as compared to PylS. This suggested that PylS Lys is involved in acylating tRNACUA and cellular tRNA while LysK and LysS are involved in acylating only cellular tRNALys. Charging tRNACUA with lysine by PylS is possibly an initial step in the mechanism of readthrough of UAG (amber) codons and encoding pyrrolysine within methylamine methyltransferases in Methanosarcinaceae. iii Dedicated to my Family iv ACKNOWLEDGMENTS I wish to thank my adviser, Joe Krzycki, for his immense support, patience and encouragement throughout the course of my graduate work. I also owe thanks to my committee members for being supportive and being there for me whenever I needed their help or suggestions. I am extremely grateful for the support and wonderful environment I got from my lab members both past and present, which was essential for me through my thesis. This work could not have been possible without the support of funding from the National Science Foundation and the Department of Energy , USA. Last but not the least I wish to thank my husband for egging me along the whole way. v VITA October 2, 1971…………………Born- Tirunelveli, India 1992…………………………… B. S. (Honours) Biochemistry, Delhi University, India 1994…………………………… M. S. Marine Biotechnology, Goa University, India 1997- 2002……………………..Graduate Teaching and Research Associate, The Ohio State University PUBLICATION 1. Srinivasan, G., C.M. James, and J.A. Krzycki, Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science, 2002. 296(5572): p. 1459-1462. FIELD OF STUDY Major Field: Microbiology vi TABLE OF CONTENTS Abstract……………………………………………………………………………………ii Dedication……………………………………...…………………………………………iv Acknowledgment………………………………………………………………………….v Vita….……………………………………………………………………………….……vi List of Figures…………………………………………………………………………….xi List of Abbreviations……………………………………………………………………xiv Chapters: 1. Introduction……..………………………………………………………………….….1 1.1 Methanogens……………………………………………………………………1 1.2 Methylamine metabolism……………………………………………………….2 1.3 Stop codon recognition to terminate translation………………………………..7 1.4 Recognition of stop codon to prevent translation termination………………..10 1.5 Natural suppressor tRNA……………………………………………………...14 1.6 Decoding the opal codon as selenocysteine…………………………………...17 1.7 Aminoacyl-tRNA synthetases………………………………………………....25 1.8 Archaeal tRNA synthetases…………………………………………………...30 1.9 Lysyl-tRNA synthetase (LysRS) ……………………………………………..31 1.10 Structural studies of lysyl-tRNA synthetase……………………………….….32 1.11 Summary of the work described in this thesis………………………………...38 2. Examination of genes encoding monomethylamine methyltransferase and its cognate corrinoid protein (mtmCB) of M. barkeri MS……………………………....40 vii 2.1 Introduction………………………………………………………………………40 2.2 Materials and Methods……………………………………………...……………44 2.2.1 Nucleotide sequence accession numbers………………………………...44 2.2.2 Organisms………………………………………………………………..44 2.2.3 Isolation of nucleic acids………………………………………………...44 2.2.4 RNA isolations and Northern hybridizations…………………………….44 2.2.5 Quantitation of MMA in the growth media……………………………...45 2.2.6 Cloning of mtmC2B2 and its flanking regions…………………………..46 2.2.7 Sequencing methods……………………………………………………..46 2.2.8 Mapping of the transcription start site…………………………………...47 2.2.9 Analysis of mtmB2 transcript around the UAG codon………………......47 2.2.10 Computer-aided sequence analysis………………...…………………….48 2.3 Results……………………………………………………………………………49 2.3.1 Cloning and sequencing of mtmC2B2 and flanking regions……..………49 2.3.2 Comparison of the transcription patterns of mtm1 and mtm2 when grown on TMA, MMA or methanol as substrate. ………………………50 2.3.3 Cells grown on methanol produce and consume MMA. ………………..52 2.3.4 Mapping of the mtm2 transcript start site. ………………………………55 2.3.5 Presence of the amber codon in transcripts encoding mtmB2……………56 2.4 Discussion………………………………………………………………………..59 3. Amber decoding tRNA and its cognate tRNA synthetase from M. barkeri MS…….66 3.1 Introduction………………………………………………………………………66 3.2 Materials and Methods…………………..……………………………………….67 3.2.1 Organisms and culture…………..……………………………………….67 3.2.2 Isolation of DNA and total RNA…………..…………………………….67 3.2.3 Total tRNA pool preparation…………..………………………………...68 3.2.4 Sequencing of pylTSBC…………..……………………………………...69 3.2.5 Recombinant expression and purification of PylS..……………………...69 3.2.6 Preparation of in vitro transcribed tRNACUA………..…………………...70 3.2.7 Assay of LysRS activity……………………..…………………….……..71 3.2.8 tRNAscan-SE method to identify tRNA from a given sequence….……..72 viii 3.3 Results……………………………………………………………………………73 3.3.1 Search for an amber decoding tRNA in the unannotated M. barkeri Fusaro genome database…………………………………………………73 3.3.2 Secondary Structure of pylT encoded amber tRNA……………………...73 3.3.3 Northern analysis of pylTSBC genes……………………………………..75 3.3.4 Analysis of regions upstream of pylT and pylS…………………………..75 3.3.5 Analyses of homologs of pylTSBCD in D. hafniense……………………76 3.3.6 Analysis of the pylS gene………………….………………….………….79 3.3.7 Cloning and expression of pylS in E. coli………………….………….…81 3.3.8 Aminoacylation assay with recombinant PylS…………………………..81 3.3.9 Aminoacylation of tRNACUA by PylS………………….………………. 84 3.4 Discussion………………….………………….………………….……………..85 4. Expression of the three lysyl tRNA synthetase genes from M. barkeri MS………...89 4.1 Introduction………………….………………….………………….…………...89 4.2 Materials and Methods………………….………………….…………………...90 4.2.1 Organisms………………….………………….………………….…….90 4.2.2 Isolation of DNA and tRNA………………….………….……….…….91 4.2.3 Cloning and sequencing of M. barkeri lysS, lysK and lysM genes……..91 4.2.4 Recombinant expression and purification of LysK, LysS and PylS……93 4.2.5 Assay of LysRS activity………………….……………………….…….94 4.2.6 RNA isolation and Northern hybridizations…………………….……...95 4.2.7 Mapping of lysKM transcript…………….……………………….…….95 4.2.8 Nucleotide sequence accession numbers and similarity searches...…….95 4.2.9 Preparation of in vitro transcripts of tRNACUA………………………....96 4.3 Results…………………………………………………………………………..96 4.3.1 The class I lysyl-tRNA synthetase gene in Methanosarcina spp………96 4.3.2 The class II LysRS of Methanosarcina spp……………………………98 4.3.3 Transcripts of lysK detectable during early log growth on MMA, but not methanol………………………………………...……………...98 4.3.4 Transcripts of lysS are detectable in all phases of growth on methylamine and methanol……………………………………………..100 ix 4.3.5 The pylTSBC transcript is detectable throughout growth on MMA or methanol…………………………………………………..100 4.3.6 Transcripts of kamA are made during early logarithmic phase when grown on MMA, but not methanol……………………………….101 4.3.7 Mapping of the lysKM transcript start site……………………………...101 4.3.8 Recombinant expression of M. barkeri lysK and lysS genes in E. coli………………………………………………………………...105 4.3.9 Aminoacylation of in vitro pylT transcript by LysK, LysS and PylS………………………………………………………………...110 4.4 Discussion………………………………………………………………………111 5. Perspective……………………………………………………………………….…115 Bibliography……………………………………………………………………………122 x LIST OF FIGURES Figures Pages 1.1 The 16S rRNA phylogenetic tree showing the distribution of methanogens within the archaeal domain……………………………..2 1.2 Pathways of methanogenesis………………………………………….4
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