Quality Assurance Notes:
Strain IDs:
TIGR4:SPN#####
R6: spr####
G54: SP####

R6 and G54 strains were found using alternate names: R6: ATCC BAA-255, G54: serotype 19F

Group Presentation

Individual Assignment

1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries. Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources.

beta-hemolytic: test performed on blood agar showing lysis of red blood cells. Hemolysis refers to the release of hemoglobin when red blood cells break open. (http://www.biology-online.org)
contigs: casual term referring to overlapping parts of the genome. (http://www.biology-online.org)
bacteriocins: antibacterial that hurts some strains within the same bacterial family as the ones who produce it. (http://medical-dictionary.thefreedictionary.com)
sortase: "enzyme that anchors surface proteins to cell wall" of gram positive bacteria. (http://www.wikigenes.org/e/ref/e/10427003.html)
putative: generally inferred (http://medical-dictionary.thefreedictionary.com)
concomitant: joined together or accessoried. (http://medical-dictionary.thefreedictionary.com)
transposase: enzymes that codes for the insertion of transposons, a utility of bacteria. (http://www.biology-online.org)
ubiquitous: occurring in many places at once. (http://www.merriam-webster.com/dictionary)
porins: component proteins that assemble to make a pore in a membrane. (http://www.biology-online.org)
ortholog: gene found in one or many organisms with a common ancestor. (http://www.biology-online.org)

Genome of the Bacterium Streptococcus pneumoniae Strain R6 Article

Introduction

S. pneumoniae infection is a top cause of death in the U.S., ~1.1 million annually worldwide
1/3 isolates are able to resist penicillin, antibiotic resistance is increasing
Streptococcus can be either pathogenic or commensalists, requiring a eukaryotic host
the experiment sequenced the genome of S. pneumoniae with hopes that it would help find new therapies
used R6 strain, a derivative of a smooth strain, used commonly in clinical and lab settings
this strain is malleable and safe to work with

Materials/Methods Used in the Experiment

original R6 strain retrieved from an Alexander Tomasz
derived from original strain D39
R6 has ability to be converted to a strain able to resist penicillin
Genome Sequencing:
- brain heart infusion medium was used to grow cultures of bacteria, where DNA was extracted from
- used a purification process including extractions, precipitations, and spoolings
- plasmids were made using the DNA fragments
- ~44,000 sequences in total were made
- used PHRED, CONSED, and PHRAP to rejoin the DNA and analyze the sequences
- an algorithm was used in order to determine repeating patterns in the sequences
- used a process called southern blotting and PCR to analyze the plasmids and find end sequences
- located a hypothetical protein on one ORF that they predicted would be many base pairs larger than the found repeat actually was
Sequence Annotation/Analysis:
- used gene prediction programs to annotate the genome
- results were imported to database using the Microsoft SQL server
Identification of ORFs:
- used program called Glimmer to match potential ORF sequences within the genome
- assigned each sequences a gene id formatted as spr####
Gene Assignment:
- all specified ORFs were put through a BLAST search in GenBank
- also compared these with those found in Prosite library
- searches allowed for gene id finalization
RNA identification:
- RNAs identified using subsequent ribosome sequence database
Sequence was given an accession number in GenBank database

Results of Experiment

Table 1:
- original prediction that many base pairs were missing was found correct
- this caused seven expected genes to not be found
- Table 1 includes a list containing all genes found in R6 proteins
- classified as either pathogenic/virulent or protective antigen
- include genes from surface proteins, bacteriocin secretion
Figure !:
- this figure shows the metabolism of glutamine and carbohydrates, along with diagraming some cell surface proteins and substrate transport
- some of the proteins functions that they have pictured were not found
Table 2:
- lists some other genes that could potentially code for drug/antibiotic efflux pumps
- did not assume that these were contributors to virulence
Table 3:
- another list of genes that were found to be shorter than expected based on orthologs
- thought maybe these were fragmented portions of parent genes
Figure 2:
- compares R6 sequences with those of other organisms
repetitive elements found more common in 'S. pneumoniae' than any other bacteria are BOX, RUP, and IS elements (>3% of genome)
Table 4:
- looks at percentages of genes positioned certain ways next to repetitive BOX and RUP elements
Previous experiments indicate that there should be 10 IS (another repetitive element) elements present in the DNA, but in the experiment only 3 were identified.
suggested that insertion of IS elements may ultimately affect BOX and RUP ratios in the 3'-3' and 5'-5' ends on opposite chromosomes
did not find an expected IS1202 element in R6 strain that was found in parent D39 strain
found all expected induced genes for competence that was noted by reference Lee and Morrison
thought gene spr1098 coded for sortase, conflicted with previous study by Pallen and colleagues

MOD: SpR6

http://www.streppneumoniae.com
main links are 'analysis' and 'contact us'
information content available on website is: nucleotide sequences, strain and specific gene info, medical relevance of the strain, strain metabolism, sequences of predicted ORFs, repeat elements, and RNA sequences
metadatabase, uses other databases as source for search information
electronically curated, with minimal manual updates
Director is Elliot Lefkowits
run by Molecular and Genetic Bioinformatics Facility at University of Alabama at Birmingham
funded by:
- UAB Center for AIDS Research (1991-2008)
- UAB Health Services Foundation General Endowment Fund (2001-2004)
no license on database
information available through database is public information, therefore no restrictions on use
Updates:
- no visible updates could be found
- copyright for site is 2001
- UAB information page last updated February 17, 2005
there are links to the CDC and GenBank databases
Sequence information can be fully downloaded for free as FastA files
Appearance/User Friendliness:
- Overall simplistic, visually appealing
- easy to navigate, well-organized for the most part
- no help section or tutorial
- when making a sample search, information was easy to follow and find, results were clearly presented
- organized in table/column form
- gene id's were presented in following form: spr####