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MERLOT II


    

Learning Exercise


Material: TIGR: The Institute for Genomic Research
Submitted by: Judith Kandel on Aug 08, 2002
Date Last Modified: Aug 08, 2002
Title: Microbial Milestones: Genome Sequencing
Description: Students will use the TIGR database to investigate the genome of Escherichia coli. In addition, they will compare selected genes in E. coli to another prokaryote
Type of Task: Core activity, Individual, Student-centered, Unsupervised
Time Required 2 hours
Topics: Bacterial genetic information
Course: Microbiology, Molecular BIology
Audience: College Upper Division
Categories:
Prerequisites Skills: Understanding structure and function of bacteria including gene structure and regulation
Learning Objectives: To relate information on an organism's structure/function to its genetic composition
To introduce the TIGR database and learn some basic queries
Text of Learning Exercise:

 











Microbial
Milestone: Genome Sequencing


Understanding E. coli



 



The genome represents all the structures that an organism can
create, all the metabolic reactions that it can perform, and all the
strategies that it can use to adapt to its environment. The genome
tells us what the organism can and cannot do.



The first complete microbial genome sequence was published in
1993. The organism was Haemophilus influenzae, a commensal
resident of the upper respiratory tract and etiological agent of
otitis media (middle ear infection) and respiratory infections,
primarily in children.



When a genome is sequenced, every gene is assigned to a category
according to its function. Included are categories for genes with
unkown function
(those known to produce proteins but the function
of the protein has not been identified) and hypothetical genes
(those that appear to be genes because they contain the appropriate
elements of a gene but no protein product has yet been identified in
the cell). The hypothetical genes are further divided into two parts
- those that are present in more than one organism (conserved
hypothetical genes) and those that are unique to a single organism.
The following table lists the categories that are used to describe
prolaryotic genes.






























































 Category - Functional Roles of Genes



Amino acid biosynthesis



Biosynthesis of cofactors, prosthetic groups, and
carriers



Cell envelope (cell wall and surface structures)



Cellular processes (cell division, chemotaxis,
conjugation, pathogenesis)



Central intermediary metabolism (N, P, S one C
compounds)



DNA metabolism



Energy metabolism



Fatty acid and phospholipid metabolism



Hypothetical proteins



Other categories (plasmid, prophage functions)



Protein fate (folding, secretion, degradation)



Protein synthesis



Purines, pyrimidines, nucleosides, and nucleotides



Regulatory functions



Signal transduction (PTS, two component systems)



Transcription



Transport and binding proteins



Unknown function





 In this exercise, you will investigate the genome of
Escherichia coli, the bacterium most studied in the laboratory
whose sequence was published in 2001. In addition, you will compare
E. coli to another prokaryote.



You will access The Institute for Genomic Research (TIGR) website,
which publishes information on all completed microbial sequences.



http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl



Select E. coli K12-MG1655 from the genome pages
menu



Click on Overview found on the navigation bar at the top of
the page



Scroll down and click on DNA Molecule Information. What is the
construction of the genome?
Return to the previous page.



Click on Role Category Graph - this should bring up a graph
and a table of the distribution of genes according to category.



Answer the following questions




  • Of the known genes, which category has the most genes? How
    many?


  • Which category has the least genes? How many?


  • How many genes have functions that are unknown? What percent
    of the genome do they represent?



Search for specific genes by clicking on the search function of
the menu bar.



Tryptophan operon by searching for trpR

Lactose operon by searching for lacI (this is the lac
repressor)



Phosphotransferase system by searching for Hpr




  • Chemotaxis and motility by seraching for CheY and Fla

    Aerobic survival by searching for superoxide dismutase



    Select any other gene of your choice




  • Return to the main TIGR page and select another sequenced
    prokaryote genome as indicated.



    Aeropyrum pernix K1



  • Aquifex aeolicus VF5

    Archaeoglobus fulgidus DSM4304



    Bacillus halodurans C-125



    Bacillus subtilis 168



    Borrelia burgdorferi B31



    Buchnera sp. APS



    Campylobacter jejuni NCTC 11168



    Caulobacter crescentus CB15



    Chlamydia pneumoniae AR39



    Chlamydia pneumoniae CWL029



    Chlamydia pneumoniae J138



    Chlamydia trachomatis MOPN



    Chlamydia trachomatis serovar D



    Deinococcus radiodurans R1



    Enterococcus faecalis V583



    Escherichia c oli K12-MG1655



    Escherichia coli O157:H7 (EDL933)



    Escherichia coli O157:H7 (VT2-Sakai)



    Haemophilus influenzae KW20



    Halobacterium sp. NRC-1



    Helicobacter pylori 26695



    Helicobacter pylori J99



    Lactococcus lactis subsp. lactis IL1403



    Magnetococcus MC-1



    Mesorhizobium loti



    Methanobacterium thermoautotrophicum delta H



    Methanococcus jannaschii DSM 2661



    Mycobacterium leprae TN



    Mycobacterium tuberculosis CDC1551



    Mycobacterium tuberculosis H37Rv (lab strain)



    Mycoplasma genitalium G-37



    Mycoplasma pneumoniae M129



    Mycoplasma pulmonis UAB CTIP



    Neisseria meningitidis MC58



    Neisseria meningitidis Z2491



    Pasteurella multocida PM70



    Porphyromonas gingivalis



    Pseudomonas aeruginosa PAO1



    Pyrococcus abyssi GE5



    Pyrococcus horikoshii (shinkaj) OT3



    Rickettsia prowazekii Madrid E



    Staphylococcus aureus COL



    Staphylococcus aureus Mu50



    Staphylococcus aureus N315



    Streptococcus pneumoniae TIGR4



    Streptococcus pneumoniae strain R6



    Streptococcus pyogenes M1



    Sulfolobus solfataricus P2



    Synechocystis sp. PCC 6803



    Thermoplasma acidophilum DSM 1728



    Thermoplasma volcanium GSS1



    Thermotoga maritima MSB8



    Treponema pallidum Nichols



    Ureaplasma urealyticum serovar 3



    Vibrio cholerae El Tor N16961



    Xylella fastidiosa 9a5c



     





  • Briefly describe the organism providing its taxonomic position,
    its genome size and construction, morphology, gram reaction,
    nutritional mode, and any pathogenic activities. This information can
    often be found by clicking on Background Information.



    Repeat your analysis as you did for E. coli.



    Click on Role Category Graph - this should bring up a graph
    and a table of the distribution of genes according to category.



    Answer the following questions




    • Of the known genes, which category has the most genes? How
      many?


    • Which category has the least genes? How many?


    • How many genes have functions that are unknown? What percent
      of thegenome do they represent?


    • How does this compare to E. coli?



    Search for specific genes by clicking on the search function of
    the menu bar. Indicate if these genes are present and how the results
    are consistent with your knowledge of the organism.



    Tryptophan operon by searching for trpR

    Lactose operon by searching for lacI (this is the lac
    repressor)



    Phosphotransferase system by searching for Hpr




  • Chemotaxis and motility by seraching for CheY and Fla

    Aerobic survival by searching for superoxide dismutase



    Your personally selected gene (gene1).



    Try another gene that you would expect to find in this organism
    but not in E. coli (Gene 2)




  • Complete the following and submit



    1. Description of assigned organism

    2.





















    Organism



    Most genes category/number



    Least genes category/number



    Percent with unknown functions



    E.coli



















    3.

























































    GENE



    Present in E. coli?



    Present in Second organism?



    Function of Gene



    trpR









    lacI









    hpr









    cheY









    fla









    superoxide dismutase









    Gene 1-









    Gene 2-











    4. Describe how the results in question 3 are consistant with
    your knowledge of the organism.



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