Kendall High School and the Western New York Genetics in Research and Health Care Partnership

A Annotation of the Listeria monocytogenes Genome from DNA Coordinates 1450..2513 and 5886..7337 Alycia A. Davenport*, Bridget K. Miller*, and Kathryn S. Hoppe Kendall High School and the Western New York Genetics in Research and Health Care Partnership

Abstract LM5923_0009: The ini tial propo sed product of thi s gene by GENI-ACT was Listeria monocytogenesisprin cipally found in pathogenic ca ses offood Modules ofthe GEN I-ACT (http://w w w .geni-act.org/) were used to hypothetical protein. The top BL AST hits for thi s gene were, poisoning. This organism which cause s Listeriosis, is one of the complete Listeria monocytogene s genome annotation. The however, Rhamnulokinase . The BL AS T hits had signi fi cant and leading causes of death offoodborne pathogens. The bacterium can modules are described below: spr ead from the si te of infe ction in the intestines to the nervous system scor e s and E-value s. The cor r ec t annotation being Modules Activities Questions Investigated Rhamnulokinase isalso suppor ted byTIGRFAM and PFA M hitsfor to the placenta in pregnantindividuals. The purpose of this study was Module 1- Basic Information DNA Coordinates and What is the sequence of my to identify and explain different coding regions of the genome of Module Sequence, Protein Sequence gene and protein? Where is this gene. It is thus proposed tha t LM5923_0009 should be it located in the genome? Listeria monocytogenes. The tw o gene lo ci studied were Listeria annotated asRhamnulokinase .Rhamnulokina se (EC2 .7.1 .5) isan monocytogene 5923_0009 and 5923_0004. Methods for studying Module 2- Sequence-Based Blast, CDD, T-Coffee, Is my sequence similar to enzyme tha t catal y zes the che mica l reaction ATP + L-rhamnulose Similarity Data WebLogo other sequences in \rightleftharpoons ADP + L-rhamnulose 1-phosphate . Listeria Listeria monocytogenes were the GENI-ACT online modules one Genbank? through seven. The gene annotation of locu s 5923_0009 show ed it Module 3- Structure-Based TIGR fam, P fam, P D B Are there functional domains . monocytogenes asa whole has roughly 881 genes predicted to be was an enzyme and locus 5923_0004 was a transmembrane protein. Evidence in my protein? enzymes.Listeria monocytogene s 08-5923 has an estimated 3039 Module 4- Cellular Gram Stain, TMHMM, Is my protein in the genes, of which 2966 are predicted to be protein s. Although both This study exhibited that the computer process of gene annotation was Localization Data SignalP, PSORT, Phobius cytoplasm, secreted or cor r ectly identified, even though accuracy was previously questioned. embedded in the membrane? participants in the GENI-ACT had genes from the sa me genome, each had a different locus. Introduction Module 5- Alternative Open IMG Sequence Viewer For Has the amino acid Reading Frame Alternate ORF Search sequence of my protein been called correctly by the Figure 5: WebLogo of Listeria monocytogenes 5923_0009: Throughout the whole Listeria monocytogenes 5923_0004: computer? alignment of the amino acids there is higher conservation. T here is a greater The ini tial proposed product ofthi s gene byGEN I-ACT was also a Module 6- Enzymatic KEGG, MetaCyc, E.C. In what process does my Function Number, protein take part? predominance of polar amino acids throughout the whole sequence. hypothetical protein. However , the top BL AST , CDD, and Module 7- Gene Paralog, Pseudogene Are there other forms of my TIGRFAM hits suggested thi s gene was membrane protein Duplication/Gene gene in the bacterium? Is Degradation my gene functional? insertase YidC . YidC is required for the insertion and/or proper folding and /or comple x for mation of in tegral inner membrane proteins. The cellualr loca liza tion module predicted LM5923_0004 Results to be a tran smembrane protein . All toge ther, the existence of well put together fun ctional do mains, trans membrane topography , and the cell lo cation within the amino acid sequen ce wa s con fir med by the participants data . The annotation ofthi s gene should therefore be membrane protein insertase YidC. Figure 1: Listeria monocytogenes Conclusions

Listeria monocytogenes is a facul tati ve anaerobic, mo tile , Throughoutthi s study the GENI-ACTgu ided the participan ts through encapsulated, and non-spor e forming gram po sitive rod-shaped the gene annotation. Evidence wa s found tha t bo th genes, which bacterium, found predominantlyin a biofilm formation.Thi sba cterium is were originallyanno tated ashypotheticalproteins on their respe citve catalase-positive and oxidase-negative. It was fir st isolated in 1924 by Figure 2: A TMHMM result for Listeria monocytogenes 5923_0004 predicts six GENI-ACT gene infor mation pages, had better had better call s E.D.G. Murray, but originally tit led Bac terium monocytogenes. It was transmembran e helixes. based on our resear ch. The gene annotation pro vided signi fi can t reverted back to the know n name ofListeria monocytogenesby Harvey data for the Listeria mono cytogenes in cluding the unique shape and Pirie in 1940. It wasrelated to neonatalinfe ction, sep sis , and meningitis Figure 3: A size ofthe gene be tween the tw o participants different model s. The in Eas t Germany in 1952.Listeria monocytogeneswas announced asa SignalP output tw o genes annotated were LM5923_0009 and LM monocytogenes foodborne illness30 year s later in Nova Scot ia.Listeria monocytogenes for Listeria Figure 6: PF AM results of Listeria monocytogenes 5923_0009 (T op and 5923_0004. We propose that LM5923_0009 should be anno tated growsabundantlyat temperatures of four to thirt y degrees celsiu s. Four monocytogene bottom left). Key structural residues in the HMM logo for FGGY_C include asRhamnulokina se and tha t LM5923_0004 should be annotated as additionalvitam ins including riboflavin, thiamine, bio tin,and thioc tic acid s 5923_0004 G6, T7, A126, G157, A170, G189, and A194 Bottom right).. shows the and sever al other amino acids are needed for Listeria monocytogenes membrane protein insertase YidC. presence of a to grow. signal peptide. References Listeria monocytogenes is relevant in multiple ca ses across the Sims et al. (2009). Complete genome sequence of Listeria monocytogenes . scienti fi c communi ty . Initiall y found in case s of adolescent rabbits, it is Standards in Genomic Sciences, 12 - 20. most recently found in food poisoning case s, and studies with Listeria. (n.d.). Retrieved May 24, 2016, from http://www.foodsaf ety. gov /poi soni ng /ca uses /bacteriaviruses/li ste ria/ pancreatic can cer with radioactive Listeria monocytogenes. Listeria Paterson, & Maciaqi. (2005, October 7). Listeria-based vaccines for cancer monocytogenes isabundantly found in dairy products and vegetables . treatment. One of the most recent case s of Listeria mono cytogenes, was a Figure 4: A phobius U.S. Food and Drug Administration. (n.d.). Retrieved May 24, 2016, from multistate outbreak in raw milk in Miller’s Organic Farm in output of Listeria http://www.fda.gov/Fo od /Rec allsO utb reaksE mergenci es/O ut bre aks/ uc m3 59 588 .ht m Pennsyl vania, as of March 2016. It is recommended that people monocytogenes 5923_0004 showing the Acknowledg ments consume pasteurized dairy products for this reason, the utmost safe ty presence of five for our people. Listeria monocytogenes has been in vestiga ted in using transmembran e helixes Supported by an NIH Science Education Partnership (SEPA) Award -5R25OD0105 Nontoxic Radioactive Listeria as a highly effective therapy against and a signal peptide. Figure 7: Example FGGY family of Carbohydrate Kinases, N-terminal domain. pancreatic cancer . Listeria monocytogenes was used in presenting to Specifically, Enterococcus casseliflavus glycerol kinase complexed with glycerol Dr.Stephen Koury (University of Buffalo) tumor associated antigen s, and was su cce ss ful in efficiently clear ing Tige E. Noni (teacher at KCS) the immune system ofpathogens.