Mrub_1199 & Mrub_2272 of \u3cem\u3eMeiothermus ruber\u3c/em\u3e are orthologous genes to the b0262 gene in \u3cem\u3eEscherichia coli\u3c/em\u3e while Mrub_1200, Mrub_1201, Mrub_2015 & Mrub_2271 are not orthologous to the b0262 gene coding for the Iron (Fe3+) ABC Transport System

In this project we investigated the biological function of the genes Mrub_1199, Mrub_1200, Mrub_1201, Mrub_2015, Mrub_2271 and Mrub_2272 (KEGG map number 02010). We predict these genes encode components of an Iron (Fe3+) ATP Binding Cassette (ABC) transporter: 1) Mrub_1199 (DNA coordinates [1211595-1212572] on the reverse strand) encodes the permease component (aka transmembrane domain); and 2) Mrub_1200 (DNA coordinates [1212612-1214093] on the reverse strand) encodes the ATP-binding domain (aka nucleotide binding domain); and 3) Mrub_1201 (DNA coordinates [1214347-1215309] on the reverse strand) encodes the substrate binding protein (aka the periplasmic component); and Mrub_2015 ( DNA coordinates [2053963-2054949] on the reverse strand) encodes the substrate binding protein (aka the periplasmic component); and Mrub_2271 (DNA coordinates [2319980-2321551] on the forward strand) encodes the permease component (aka transmembrane domain); and Mrub_2272 (DNA coordinates [2321548-2322639] on the forward strand) encodes the ATP-binding domain (aka nucleotide binding domain). This transport system is found in E. coli K12 MG1655 as the gene afuC (locus tag b0262(DNA coordinates [277756..278802] on the reverse strand) encoding the ABC transporter system for Iron. The afuC gene is the only gene coding for the Iron transport system while M. ruber has genes for all the components. The genes coding for the permease domain and substrate binding protein seem to be absent in E. coli. This project is part of the Meiothermus ruber genome analysis project, which predicts gene function using the bioinformatics tools collected under the umbrella of the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT)

Isolating Antibiotic-producing Bacteria From Soil

As the antibiotic crisis becomes stronger, we are in need of finding more novel antibiotics. This project is a collaboration with the Tiny Earth Project Initiative (TEPI), which is a global network of educators and students focused on student sourcing antibiotic discovery from soil. The soil isolates were determined to be part of the Bacillus and Pseudomonas genus

Effects of Temperature on CRISPR/Cas System

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the effect of temperature on the complexity of CRISPR/Cas systems in bacterial organisms across temperature classifications. We predict that temperature extremes would result in CRISPR/Cas systems with multiple operons, repeating cas genes, and complex systems. CRISPR/Cas systems can be classified into three types with a number of subtypes based on the CRISPR-associated genes, cas genes, present in a given organism. Our hypothesis is supported by the presence of multiple operons in thermophilic organisms based on data collect with bioinformatic tools KEGG and IMG/M. Organisms were predicted to have functional CRISPR/Cas operons, cas genes, or CRISPR arrays which suggest the presence of a CRISPR/Cas system

Antibiotic Producing Microbes Found in Soil

The antibiotic crisis is a growing concern as more and more diseases are becoming untreatable due to antibiotic resistance. Of all antibiotic resistant bacteria, the ESKAPE strains are the most dangerous because of their association with higher mortality rates and multidrug resistance. In this study, ESKAPE-like strains will be studied as they are similar to the ESKAPE strains and provide comparable data in a safe manner. Soil samples are evaluated to test the presence of any microbes that may be antibiotic producers. This project is in collaboration with the Tiny Earth Project Initiative (TEPI), which is a global network of educators and students focused on student sourcing antibiotic discovery from soil. Two antibiotic producing strains were confirmed, sequenced, and identified using the BLAST database

Pseudomonas and Bacillus as Potential Sources of Novel Antibiotics

With an increase in antibiotic resistance within the medical field the need for novel antibiotics is evident. Through collaboration with the Tiny Earth Project Initiative, we hope to find novel antibiotics through bacteria found in soil. We were able to successfully isolate two microbes that showed broad spectrum antibiotics against both Staphylococcus epidermis and Bacillus subtilis. Through further exploration and collaboration with the Tiny Earth Project Initiative, we might be able to discover novel antibiotics

\u3cem\u3eMeiothermus ruber\u3c/em\u3e 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 \u3cem\u3eEscherichia coli\u3c/em\u3e, which encode for components of an ABC transporter involved in sn-glycerol - 3-phosphate

In this project we investigated the biological function of the genes mrub_0320, mrub_0321, mrub_0322, and mrub_2366 (KEGG map number 02010). We predict these genes encode components of a sn-glycerol-3-phosphate (ABC) transporter: 1) mrub_0320 (DNA coordinates 288469..289401) encodes the permease component (aka transmembrane domain), predicted to be an ortholog; 2) mrub_0321 (DNA coordinates 289394..290218) encodes another permease domain, and also contains a transcriptional regular; ATP-binding domain (aka nucleotide binding domain); 3) mrub_0322 (DNA coordinates 290234..291541) encodes the solute binding protein; and 4) mrub_2366 (DNA coordinates 2418207..2419352 on the reverse strand) encodes for an ATP-binding domain for multiple sugar-related ABC transport systems (aka nucleotide binding domain). The unique function of mrub_2366 is not found in the E. coli ortholog; for that series of genes, the ATP-binding domain is ABC transporter specific. Since the ATP-binding domain for M. ruber has less specificity, it is not a part of the operon of the rest of the sn-glycerol-3-phosphate ABC transporter. This project is part of the Meiothermus ruber genome analysis project, which predicts gene function using the bioinformatics tools collected under the umbrella of the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT)

\u3cem\u3eMeiothermus ruber\u3c/em\u3e Mrub_0976 and Mrub_1641 share the same functions as \u3cem\u3eEscherichia coli\u3c/em\u3e b3940 and b3433 in the biosynthesis of homoserine

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_0976 and Mrub_1641. We predict that Mrub_0976 encodes the enzyme aspartate kinase (DNA coordinates 964404..965630) which is the 1st step of the homoserine biosynthesispathway (KEGG map number M00018). It catalyzes the conversion L-aspartate to L-asparyl-4-phospate. The E. coli K12 MG1655 ortholog is predicted to be b3940, which has the gene identifier ‘thrA’. We predict that Mrub_1641 encodes the enzyme aspartate-semialdehyde dehydrogenase (DNA coordinates 1672219..1673217) which is the 2nd step of the homoserine biosynthesispathway (KEGG map number M00018). It catalyzes the conversion of L-asparyl-4-phospate to L-aspartate-semialdehyde. The E. coli K12 MG1655 ortholog is predicted to be b3433

Mrub_2874 is homologous to b3386 and Mrub_1349 is homologous to b2914, but Mrub_1349 is not homologous to b4090

ABSTRACT. This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2874 and Mrub_1349. We predict that Mrub_2874 encodes the enzyme ribulose-5-phosphate 3-epimerase (DNA coordinates 2912530..2913204 on the reverse strand), which is the first step of the pentose phosphate pathway (KEGG map number 00030). It catalyzes the conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b3386, which has the gene identifier rpe. We predict that Mrub_1349 encodes the enzyme ribose-5-phosphate isomerase (DNA coordinates 1381292..1381978 on the reverse strand), which is also the first step of the pentose phosphate pathway (KEGG map number 00030). It catalyzes the conversion of D-ribulose 5-phosphate to D-ribose 5-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b2914 and b4090, which have the gene identifiers rpiA and rpiB respectively. The comparison of Mrub_2875 to b3386 and the comparison of Mrub_1349 to b2914 were conclusive, but the data was inconclusive when comparing Mrub_1349 to b4090

Mrub_3015 is orthologous to the b2757 gene found in \u3cem\u3eEscherichia coli\u3c/em\u3e coding for casD

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of the gene Mrub_3015, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system. We predict that Mrub_3015 (DNA coordinates 3055550...3056245) encodes the the CRISPR-associated protein cas5, which is integral in maintaining the crRNA-DNA structure, keeping the complex from base pairing with the target phage DNA. Our hypothesis is supported by identical hits for Mrub_3015 and b2527 to the KEGG, Pfam, TIGRfam, CDD and PDB databases as well as a low E-value for a pairwise NCBI BLAST comparison. Both protein products are predicted to be localized in the cytoplasm. Finally, both proteins share numerous highly conserved amino acids, when compared to the consensus sequence of Pfam domains PF09704, PF18019, and PF00270

Mrub_3018 is Orthologous to \u3cem\u3eE. coli\u3c/em\u3e B2759 (casB)

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We studied the biological activity of the Mrub_3018 gene, which we hypothesize is orthologous to E. coli gene B2759. We predicted that Mrub_3018(DNA coordinates 3057916… 3058524) encodes the protein CasB. CasB is a protein in the CRISPR CASCADE that will function as a structural protein. When the rest of the proteins form an “S” formation CasB will connect the front and back of the “S” creating a back bone for the structure. It will help bind DNA while other proteins like Cas3 degrade the protein. The hypothesis was proven by identical hits in KEGG, COG, Pfam, TIGRfam, and PDB, as well as similar location(Cytoplasm) found using PSORT-B, PRED and TMHMM. The genes were also found to be part of an operon as they were flanked by genes that are in the CRISPR system