The goal of the M. ruber genome analysis project is to study the genes and genome organization of the bacterium Meiothermus ruber, a thermophilic bacterium found in hot springs and a few warm artificial environments. The M. ruber genome was sequenced as part of the Department of Energy Joint Genome Institute’s GEBA project (Wu et al.,2009), the goal for which was to broaden our understanding of microbial genome structure and function across the microbial Tree of Life.

The M. ruber project gives students an authentic research experience in genome analysis by performing: 1) gene annotations - using bioinformatics tools to study gene function, and 2) functional genomics - using benchtop tools common to a molecular biology lab to study gene function. The papers uploaded into this site reflect student work in both these fields of study. Students perform these projects as part of the course Molecular Genetics/BIOL375 or as independent research experiences.

Wu D et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009 Dec 24;462(7276):1056-60. doi: 10.1038/nature08656.

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Submissions from 2018

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Functional studies of the E. coli proC and a putative ortholog Mrub_1345, Mourin Azar and Dr. Lori Scott

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Mrub_0680, Mrub_0836, and Mrub_0837 found to be orthologous to E. coli CcmA, CcmB, and CcmC, respectively, coding for ABC-transport proteins involved in cytochrome-C biogenesis, Sarah N. Church and Dr. Lori Scott

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Mrub_1283, Mrub_1284 and Mrub_1285 encode for a glycine/betaine ABC transporter and are orthologs of E. coli proV, proW and proX, Lan Dang and Dr. Lori Scott

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Mrub_2836, Mrub_1595, and Mrub_1596 are orthologs of b_1857, b_1859 and b_1858 in Escherichia Coli Coding for a Zinc Uptake ABC Transporter System, Austin J. Dollmeyer and Dr. Lori Scott

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Meiothermus ruber mrub_0320 gene is an ortholog of the b3452 gene, mrub_0321 gene is an ortholog of the b3451 gene, mrub_0322 gene is an ortholog of the b3453 gene, mrub_2366 gene is an ortholog of the b3450 gene found in Escherichia coli, which encode for components of an ABC transporter involved in sn-glycerol - 3-phosphate, Jenna Hall and Dr. Lori Scott

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Mrub_1199 & Mrub_2272 of Meiothermus ruber are orthologous genes to the b0262 gene in Escherichia coli while Mrub_1200, Mrub_1201, Mrub_2015 & Mrub_2271 are not orthologous to the b0262 gene coding for the Iron (Fe3+) ABC Transport System, Kumail Hussain and Dr. Lori Scott

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Mrub_2120, Mrub_2121, Mrub_2122, Mrub_2123 and Mrub_2124 are orthologs of E. coli genes b3458, b3457, b3456, b3455 and b3454, respectively, and make up an operon that codes for the branched-chain amino acid ABC transporter in Meiothermus ruber DSM 1279, Aaron Jones, Madelyn Huber, and Dr. Lori Scott

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Examination of Orthologous Genes (Mrub_2518 and b3728, Mrub_2519 and b3727, Mrub_2520 and b3726, Mrub_2521 and b3725) Responsible for ABC Phosphate Transporters in Two Species M. ruber and E. coli, Margaret Meyer and Dr. Lori Scott

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Predicted ortholog pairs between E. coli and M. ruber are b3456 and mrub_2379, b3457 and mrub_2378, b3456 and mrub_2374, b3455 and mrub_2376, and b3454 and mrub2377, which each code for components of a prokaryotic-type ABC transporter for branched-chain amino acids, Elizabeth Paris, Tony Steinle, and Dr. Lori Scott

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Mrub_1675, Mrub_1676, Mrub_1677, and Mrub_1679 genes are orthologs of b_3458, b_3457, b_3456, and b_3454 genes in E. coli, respectively, coding for ABC transporters. Mrub_1678 and b_3455, though perform similar tasks, are not orthologous, Ravi Patel, Alaina Hofmann, and Dr. Lori Scott

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Confirmation that mrub_1751 is homologous to E. coli xylF, mrub_1752 is homologous to E. coli xylH, and mrub_1753 is homologous to E. coli xylG, Ben Price and Dr. Lori Scott

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Mrub_1325, Mrub_1326, Mrub_1327, and Mrub_1328 are orthologs of B_3454, B_3455, B_3457, B_3458, respectively found in Escherichia coli coding for a Branched Chain Amino Acid ATP Binding Cassette (ABC) Transporter System, Bennett Tomlin, Adam Buric, and Dr. Lori Scott

Submissions from 2017

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Annotation and Identification of Several Glycerolipid Metabolic Related Ortholog Genes; Mrub_0437, Mrub_1813 and Mrub_2759 In The Organism Meithermus Ruber and Their Predicted Respective Orthologs b3926, b4042 and BO514 Found In E.coli., Abdul Rahman Abdul Kader and Dr. Lori R. Scott

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Mrub_3029, Mrub_2052, are predicted orthologs of b_0688, b_0394, while Mrub_0759 and Mrub_2365 are not predicted orthologs of b_1309, in Escherichia coli, which code for enzymes involved in starch and sucrose metabolism, Max A. Benstine and Dr. Lori R. Scott

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Mrub_0860, Mrub_0701 and Mrub_2285 are orthologous to E. coli b2892, b2562 and b3863 within the RecFOR pathway for Homologous Recombination, Bailey Englund and Dr. Lori Scott

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Mrub_1304, Mrub_2007 and Mrub_2006 are orthologs of E. coli b_3189, b_3972, and b_0091, respectively within the Peptidoglycan Biosynthesis Pathway, Mylaun E. Griffith and Dr. Lori Scott

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Mrub_2052, Mrub_0628, and Mrub_2034 genes are predicted to be orthologous to b0688, b2039, and b3789 genes found in Escherichia coli, which are involved in streptomycin biosynthesis, James P. Hartnett and Dr. Lori Scott

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Serine Biosynthesis and Glycine Biosynthesis/Degradation: Mrub_0173 is Orthologous to E. coli b2913 (serA); Mrub_0125 is Orthologous to E. coli b4388 (serB); Mrub_2910 is Orthologous to E. coli b2551 (glyA)., Megan M. Janssen and Dr. Lori R. Scott

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Mrub_1873, Mrub_1872, Mrub_1871 genes are predicted orthologs of the b2285, b2284, and b2283 genes respectively, found in Escherichia coli coding for NADH ubiquinone oxidoreductase complex subunits E, F, and G., Hannah Lohmeier and Dr. Lori R. Scott

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Mrub_2642, Mrub_1054, and Mrub_1059 genes are orthologs of the Escherichia coli genes b2942, b0159, and b2687 genes, respectively, which code for methionine adenosyltransferase, adenosylhomocysteine nucleosidase, and S-ribosylhomocysteine lyase, Nicholas M. Orslini and Dr. Lori R. Scott

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Mrub_2294, Mrub_2293, and Mrub_1942 genes are orthologs of E. coli b2476, b1131, and b4006 genes, respectively, Lindsay Popp and Dr. Lori Scott

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Annotation of Genes Involved with Biosynthetic Production of Peptidoglycan within Meiothermus ruber involving supposed Orthologous Genes: Mrub_0981 and b1069, Mrub_1162 and b063, Mrub_1999 and b0084., Marckus Simmons and Dr. Lori Scott

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Mrub_1867, Mrub_1868, and Mrub_1869 genes are predicted orthologs of the b2279, b2280, and b2281 genes found in Escherichia coli coding for the NADH dehydrogenase subunits K, J, and I respectively, Wade Smith and Dr. Lori R. Scott

Submissions from 2016

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Bioinformatics Comparison of M. ruber Mrub_2507 to E. coli pdxK/b1636 and M. ruber Mrub_2888 to E. coli pdxH/b1638 to Determine the Orthologous Nature, Adam Bernardi and Dr. Lori Scott

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Comparison of genes in Meiothermus ruber and Escherichia coli in the Thiamine Biosynthesis Pathway, Erin E. Frye and Dr. Lori Scott