Download Grene Research: Virginia Tech (VT)

Grene Research: Virginia Tech (VT)
Plant Responses to the Environment, 1997- present
(Omics Work on Potatoes, Maize, Soybean, Arabidopsis, Loblolly Pine, Sitka
Spruce, in collaboration with (PIs) Hans Bohnert, (ret), Lenny Heath, Andy Pereira,
Eva Collakova, Guillaume Pilot, John McDowell, Ron Sederoff, Jason
HollidayHolliday
Pathogen
At which of these steps do we, the plant biologists, need help
from computationally savvy people?
Less voodoo, more
science?
Impediments to Discovery/Progress
RG’s Complaints
• 1. Lack of a unified, dynamic, software tool
displaying the current understanding of
signaling pathways , designed by computer
scientists for the plant biology community.
• 2. A tool that starts with input from multiple
plant biology gurus, and stores the output in a
searchable database, to be used as input for
what-if simulations that are intelligible to the
plant biology community.
Enter the Computational Guys
• Lenny Heath, CS Faculty
• Elijah Myers, Genetics, Bioinformatics, and
Computational Biology (GBCB) Grad Student
• Curtis Klumas, GBCB Grad Student
AND NSF (Beacon)
Lenny Takes Over
Gene Expression Patterns Observed
in Sitka Spruce Needles Undergoing
Winter Hardening
as analyzed in MapMan and
displayed in Beacon
Data of Dr. Jason Holliday
Department of Forestry and Environmental
Conservation
Virginia Tech
Time Course Study
• Needles were harvested for RNA isolation at
five time points, (TP0-TP4), over a period from
August – December from seedlings grown in a
common garden in British Columbia.
Hybridized to a spruce microarray.
• Samples collected for metabolite analyses
also.
Data Analysis
1. Statistically significant changes in gene expression
comparing values obtained at TP1-4 with values
obtained for TP0.
2. Dataset was loaded into MapMan, results presented
in Beacon are output from selected MapMan bins with
an in-house modification, by Elijah, and additional
functional information from PubMed.
3. Results from an in-house tool, Alpine, (Elijah, yet
again), based on filtering output from GeneMania to
display only genes that responded significantly in the
winter hardening experiment.
Example Output from MapMan : SODs,
CATS
id
at1g12520
at4g35090
at1g08830
at1g20620
description
ATCCS | ATCCS (COPPER CHAPERONE FOR
SOD1)
CAT2 | CAT2 (CATALASE 2); catalase
CSD1 | CSD1 (COPPER/ZINC SUPEROXIDE
DISMUTASE 1)
CAT3, SEN2, ATCAT3 | CAT3 (CATALASE 3);
catalase
Example Output from MapMan: Raffinose
Pathway: Gene Expression and Metabolites
At1g60470
Is galactinol
synthase
id
description
at5g20250
DIN10 raffinose synthase, sugar, cold responsive
at3g57520
AtSIP2 raffinose, phloem unloading
at1g55740
AtSIP1 putative raffinose synthase
Secretory Pathway-Associated Gene Expression
Over Time (generated from MapMan output)
Expression of Cell Wall –Associated Genes:
Output from MapMan in Heat Map Form
Some Interesting Genes Showed Large
Expression Changes (> 3 fold)
MapMan BinName
redox.ascorbate and
glutathione.ascorbate
redox.ascorbate and
glutathione.ascorbate
redox.dismutases and
catalases
redox.dismutases and
catalases
redox.glutaredoxins
hormone
metabolism.ethylene.sign
al transduction
protein.targeting.secretor
y pathway.unspecified
protein.targeting.secretor
y pathway.unspecified
id
Involved in Signaling?
at1g63940
TAPX (THYLAKOIDAL
Y (retrograde signaling,
ASCORBATE PEROXIDASE) cold)
MDAR6
monodehydroascorbate
reductase, putative
N (response to cold)
at4g35090
CAT2 (CATALASE 2)
Y? (SOS2-interacting)
at1g20620
Y? (SOS2 –interacting)
at3g02000
CAT3 (CATALASE 3)
ROXY1 disulfide
oxidoreductase
at1g50640
ERF3
Y ( ethylene)
at3g48570
SEC61 gamma subunit
N (protein processing, ER)
at5g17060
ATARFB1B; GTP binding
AGP16
(ARABINOGALACTAN
PROTEIN 16)
SUS4; UDPglycosyltransferase/
sucrose synthase
TCH4 (Touch 4)
xyloglucan:xyloglucosyl
transferase
Y (G protein signaling)
at1g77490
cell wall.cell wall
proteins.AGPs
at2g46330
major CHO
metabolism.degradation.s
ucrose.Susy
at3g43190
cell wall.modification
description
at5g57560
Y (floral development)
Y? (GPI anchor)
Y? (elicitor responsive)
N? (CBF regulon)
Observations
• Chloroplast function is manifest mainly in
antioxidant activity during winter hardening.
• Secretory pathway is very active, associated
with the expression of cell wall-related genes.
• Several “ moonlighting” genes, with both
metabolic and regulatory roles are highly up
regulated.
• Certain genes encoding central carbon
metabolism enzymes are up-regulated.
Questions
• 1. What adaptation does cell wall modification serve
during winter hardening?
• 2. What is the significance of the large increases in
the moonlighting regulatory genes?
• 3. Do these regulatory genes retain the metabolic
function of their fellow family members?
(Hexokinase 1 and invertase do, beta-amylase does
not.)
• 4. What are the characteristics of the central carbon
metabolism genes that operate at low temperatures?
CAT2 and CAT3
• Mol Cell Biol. 2007 Nov;27(22):7771-80. Epub
2007 Sep 4.
• Interaction of SOS2 with nucleoside
diphosphate kinase 2 and catalases reveals a
point of connection between salt stress and
H2O2 signaling in Arabidopsis thaliana.
• Verslues PE, Batelli G, Grillo S, Agius F, Kim YS,
Zhu J, Agarwal M, Katiyar-Agarwal S, Zhu JK.
ROXY1 – a Glutaredoxin
• Plant J. 2008 Mar;53(5):790-801. Epub 2007 Nov 23.
• ROXY1 and ROXY2, two Arabidopsis glutaredoxin genes, are
required for anther development.
• Xing S, Zachgo S.
• Mol Plant. 2012 Jul;5(4):831-40. Epub 2011 Dec 29.
• Repression of the Arabidopsis thaliana Jasmonic
Acid/Ethylene-Induced Defense Pathway by TGA-Interacting
Glutaredoxins Depends on Their C-Terminal ALWL Motif.
• Zander M, Chen S, Imkampe J, Thurow C, Gatz C.
Glutathione Reductase 1 Has a Regulatory Role
Thioredoxins Cannot Substitute
• Plant Physiol. 2010 Jul;153(3):1144-60. Epub
2010 May 20.
• Arabidopsis GLUTATHIONE REDUCTASE1 plays a
crucial role in leaf responses to intracellular
hydrogen peroxide and in ensuring appropriate
gene expression through both salicylic acid and
jasmonic acid signaling pathways.
• Mhamdi A, Hager J, Chaouch S, Queval G, Han Y,
Taconnat L, Saindrenan P, Gouia H, IssakidisBourguet E, Renou JP, Noctor G.