2015 PCB 5530 Class Projects and Grading
● Background
The projects take cutting-edge comparative genomics research into the classroom, to bring to life what
you are learning. They will train you to reason and to integrate different kinds of genomics data.
The class is split into four groups, each coordinated by a postdoctoral from our project. Groups are:
1. Riboflavin
Ghulam Hasnain
hasnaing@ufl.edu
Jerald Noble
Calvin Howard
Ze Peng
2. Lipoate
Tom Niehaus
tomniehaus@ufl.edu
Nathaniel Ellis
Scott Latimer
[Rodrigo Furtado Dos Santos]
3. Niacin
Lili Huang
lilihuang@ufl.edu
Jieying Wang
Collin LeFrois
Zhongxia Yi
4. Folate
Guillaume Beaudoin
gbeaudoin@ufl.edu
Michael Riley
Lauren Stutts
Austin Wenta
Each group will:
- First become familiar with the assigned metabolic pathways in plants and bacteria.
- Use ATTED tools to build co-expression networks for Arabidopsis genes for synthesis and salvage of
the assigned pathway, and identify genes in these networks that encode membrane proteins of unknown function. Use proteomics databases (PPDB, SUBA3) to infer the possible subcellular localization of these proteins. Such co-expressed membrane proteins are candidates for vitamin or vitamin
precursor transporters in the plasma membrane or organelle membranes of plant cells.
- Use SEED and STRING tools to identify bacterial membrane-protein genes of unknown function that
are consistently clustered with genes encoding salvage enzymes of the assigned pathway. Such
membrane-protein genes are candidates for vitamin or vitamin precursor transporters.
Each group will meet several times, under the supervision of the postdoctoral mentor, to decide the
work to be done, to review progress and to plan and prepare a single report in the format below.
Project reports. Reports should be submitted to Dr. Andrew Hanson adha@ufl.edu as an electronic file
and a good quality hard copy, by 5 pm on Friday, November 20, 2015.
Grading. For each student, 45% of the grade will be based on the performance of their group as a
whole as judged from the project report. Another 45% will be based on the postdoctoral instructor’s and
my assessment of that student’s individual contribution to the group effort (independent of the group
size). The individual contribution assessment will emphasize creativity, initiative, and quality of work, and will
also take account of the amount of work done. The final 10% of the grade will be based on contributions in
class, e.g. on questions asked or answered by the student.
Outcomes. It is anticipated that, in the best case, the groups’ predictions will form part of a publication in
a peer-reviewed journal, in which case the group members will be included as authors.
● Report format
Reports should be arranged in three sections:
1. Pathways
a. A diagram showing the metabolites, enzymes, and compartmentation of the plant synthesis and
salvage pathways. Use the format on p. 2.
b. A table listing the names and EC numbers of the enzymes involved, and giving the AGI codes
(e.g. At5g14760) for the enzymes in Arabidopsis.
2. Arabidopsis genes:
a. A table showing AGI codes of all Arabidopsis membrane-protein genes of unknown function found
in co-expression networks, the experimentally supported or predicted subcellular localization of
the proteins, and the Blast score and percent identity of the best bacterial homolog if one exists.
b. The sequence and TMHMM plot for each Arabidopsis unknown membrane-protein gene found.
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c. For one unknown membrane-protein gene (the strongest candidate if there is more than one), a
200-300 word summary of the transport function you predict, of evidence for and against this
function, and of evidence that this protein has no assigned function yet. Cite appropriate literature.
3. Bacterial genes:
a. A table listing the SEED (e.g. fig|319225.3.peg.1044) identifier of a representative of each type of
membrane-protein gene found consistently clustered with salvage genes, and the Blast score and
percent identity of the best Arabidopsis homolog if one exists.
b. The sequence and TMHMM plot for each bacterial membrane-protein gene found.
c. For one unknown membrane-protein gene (the strongest candidate if there is more than one), a
200-300 word summary of the transport function you predict, of evidence for and against this
function, and of evidence that this protein has no assigned function yet. Cite appropriate literature.
Literature citations must be in the following format:
Zheng M, Wang X, Templeton LJ, Smulski DR, LaRossa RA, Storz G (2001) DNA microarray-mediated
transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J Bacteriol 183:
4562-4570
● Report format – example of pathway diagram
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● Recommendations
Start by identifying the relevant synthesis and salvage pathways from plants and bacteria. Resources
include PlantSEED http://pubseed.theseed.org/seedviewer.cgi?page=PlantGateway and PMN (which
includes AraCyc) http://pmn.plantcyc.org/ (for plants), BioCyc http://biocyc.org/ (for all organisms) and
KEGG http://www.genome.jp/kegg/pathway.html#cofactor (for all organisms). Then draw the summary
pathway diagram.
For Arabidopsis, collect the AGI codes for all the known synthesis and salvage enzymes, and use these
to construct ATTED co-expression networks.
For bacteria, collect the sequences of salvage enzymes from model organisms (e.g. Escherichia coli,
Bacillus subtilis) and use these as entry points to search SEED and STRING for membrane-protein
genes that cluster on the chromosome with these salvage genes in diverse bacteria.
If you find an Arabidopsis transporter candidate that has homologs in bacteria, or a bacterial transporter
candidate with homologs in Arabidopsis, then use comparative genomic approaches to enrich your
prediction of the transporter’s function.
Marking scheme:
Pathway figure and tables
Arabidopsis candidate gene table
Bacterial candidate gene table
Sequences, TMHMM plots
Summaries
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