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Darin Scribner, Santiago Morales, Shady Hamdallah

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Darin Scribner, Santiago Morales, Shady Hamdallah

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  1. A project of the and the Center for Deciphering Life’s Languages at Hiram College, in collaboration with undergraduates at 10 other colleges and universities as part of the Undergraduate Research in Microbial Genome Annotation project of the U.S. Dept. of Energy Joint Genome Institute. Detailed Bioinformatics Analysis of the Histidine Biosynthesis Pathway in Planctomyces limnophilus Darin Scribner, Santiago Morales, Shady Hamdallah • Histidine biosynthesis has 10 enzymatic steps in its KEGG pathway. There are a total of seven proteins involved in histidine biosynthesis. • All of the assigned genes were found in the KEGG pathway. Based on the EC number associated for the genes, we were able to distinguish them in the pathway. Additionally, the name of the proteins helped locate the genes. For example, the hisF and hisH subunits were labeled in both the KEGG pathway and in the EC name. • Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19) and ATP phosphoribosyltransferase (EC 2.4.2.17)were in the same operon. Imidazole glycerol phosphate synthase, catalytic subunit with HisH (EC 2.4.2 subunit hisH) and phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.1.3.16) were in the same operon. Histidinol-phosphate aminotransferase and fused histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) were in the same operon (refer to sequence neighborhood). • It makes biological sense that some of the histidine synthesis genes are in the same operons because all of those genes are involved in the same pathway, so the proteins coded by those genes would most likely be synthesized together. • Only 2 genes required a change in the start codon. Gene 2500607325 was 17 amino acids shorter than 10 similar genes in related organisms (refer to T-COFFEE output below). When looking at the original start codon, an alternate start codon was found exactly 51 nucleotides upstream with a Shine-Delgarno sequence present. Additionally, gene 2500608178 was 10 amino acids longer than 10 genes found in similar organisms. When looking at the original start codon, there was an alternate start codon found exactly 30 nucleotides downstream with a Shine-Delgarno sequence. T-COFFEE Output CLUSTAL FORMAT for T-COFFEE Version_5.05 [http://www.tcoffee.org], CPU=6.17 sec, SCORE=79, Nseq=11, Len=265 2500607325 -----------------VKGVNFLNLQDAGDPVEVAARYERDGADELVFLDITASHEERG gi|167036944|ref|YP_001664522. MLAKRIIPCLDVKDGRVVKGVNFLNLKDAGDPVQIASEYNELGADELVFLDITASYEKRK gi|223489364|ref|YP_002595632. MLAKRIIPCLDVKDGRVVKGINFVNLKDAGDPVEIAERYNELGADELVFLDITASYEKRK gi|20808523|ref|NP_623694.1| MLAKRIIPCLDVKDGRVVKGINFVNLKDAGDPVEIAERYNELGADELVFLDITASYEKRK gi|78044843|ref|YP_359936.1| MLTVRIIPCLDVNKGRVVKGVNFLNLVDAGDPVELAAFYDREGADEVVFLDITASFEGRQ gi|169831774|ref|YP_001717756. MLAKRIIPCLDVNRGRVVKGVNFVNLRDAGDPVELAAVYDREGADEVVFLDITASAEGRD gi|149176453|ref|ZP_01855067.1 MLAKRIIPCLDVHAGRVVKGVNFLNLQDAGDPVEVAARYEEQGADELVFLDITASHEERE gi|32476254|ref|NP_869248.1| MLSARVIPCLDVHGGRVVKGTNFVNLRDAGDPVEVARRYEAEGADELVFLDITASHEERA gi|87308764|ref|ZP_01090903.1 MLTKRIIPCLDVKGGRVVKGVQFLELRDAGDPVEIAEIYDRQGADELTFLDITASSDERD gi|118581458|ref|YP_902708.1| MLAHRVIPCLDVDRGRVVKGTNFVNLRDAGDPVQVASRYEQEGADELVFLDICASHEERA gi|39998185|ref|NP_954136.1 MLTKRIIPCLDVKGGRVVKGVQFLELRDAGDPVEIAELYDRQGADELTFLDITASSDERS *** :*::* ******::* *: ****:.**** ** : * • There was no evidence of horizontal gene transfer in any of our annotated genes. • It was interesting that 2 start codons had to be changed. Moreover, another unique feature of the histidine biosynthesis pathway is that the biosynthesis of purine is also involved. • References: • Alifano, P., R. Fani, P. Lio, A. Lazcano, M. Bazzicalupo, M. S. Carlomagno, and C. B. Bruni, 1996. Histidine Biosynthetic Pathway and Genes: Structure, Regulation, and Evolution. Microbiology Reviews 60: 44-69. • Gene Sequence Viewer (OID=2500606649), Integrated Microbial Genomes Education Site, img-act.jgi-psf.org. • Histidine Biosynthesis KEGG Map, Integrated Microbial Genomes Education Site, img-act.jgi-psf.org. • T-COFFEE Sequence Alignment, Ebi.ac.uk/Tools/t-coffee/index.html, European Bioinformatics Institute.

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