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.
Submissions from 2019
Mrub_3014 is orthologous to b2756, Samir Abdelkarim and Dr. Lori Scott
Effects of Temperature on CRISPR/Cas System, Eddie Beckom and Dr. Lori Scott
M. ruber Mrub_3013 is Orthologous to E. coli b2755, Laura Butcher and Dr. Lori Scott
Mrub_3015 is orthologous to the b2757 gene found in Escherichia coli coding for casD, Ramona Collins and Dr. Lori Scott
Mrub_3020, a paralog of mrub_1489, is orthologous to E. coli casC (locus tag b2761), Alfred Dei-Ampeh and Dr. Lori Scott
An investigation into the relationship between mrub_3013, mrub_1477, and mrub_0224: Are they paralogs?, Melette DeVore and Dr. Lori Scott
Mrub_3019 casA gene is an ortholog to E. coli b2760, Kelsey Heiland and Dr. Lori Scott
Mrub_3018 is Orthologous to E. coli B2759 (casB), Kyle Parker and Dr. Lori Scott
Submissions from 2018
Functional studies of the E. coli proC and a putative ortholog Mrub_1345, Maureen Azar and Dr. Lori Scott
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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