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22 Φεβ 2013 (πριν από 4 χρόνια και 3 μήνες)

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3/18/2013

©T. C. Hazen #
1

Center for

Environmental

Biotechnology

Rapid deduction of bacteria stress
response pathways: Genomics,
proteomics, metabolomics and
bioinformatics

Terry C. Hazen & Adam Arkin

University of California, Berkeley

Lawrence Berkeley National Laboratory

Berkeley, California 94720

3/18/2013

©T. C. Hazen #
2

Center for

Environmental

Biotechnology

Workshop Schedule

8:30
-
9:00

Introduction



Terry Hazen, Lawrence Berkeley National Laboratory, Berkeley, CA

9:00
-
10:15

Environmental stress responses in metal
-
reducers



David Stahl, University of Washington, Seattle, WA

10:15
-
10:45

BREAK

10:45
-
12:00

Genomic microarrays to determine stress responses



Joe Zhou, Oak Ridge National Laboratory, Oak Ridge, TN

12:00
-
1:00

LUNCH

1:00
-
2:15

Proteomics of stress



Martin Keller, Diversa Corporation, San Diego, CA

2:15
-
3:30

Metabolomics of stress



Jay Keasling, University of California/LBNL, Berkeley, CA

3:30
-
3:45

BREAK

3:45
-
5:00

Bioinformatics to determine stress responses



Adam Arkin, University of California/LBNL, Berkeley, CA

3/18/2013

©T. C. Hazen #
3

Center for

Environmental

Biotechnology


Human Genome Project started in 1986


Scientific project of the millennia


Great advances in sequencing throughput


Since 1995 >150 microorganisms have been
sequenced, >100 in the last 2 years


TIGR discovers 1.2 million new bacteria/archea
genes in the Sargasso Sea March 2, 2004


The current Joint Genome Institute throughput
is ~2.0
-
2.5 billion bases per month


In theory, JGI could sequence >400 microbes
per year*, In practice, this would be very difficult
to achieve


JGI will sequence >100 microbes this year

Genomics
-

How far we have come!

3/18/2013

©T. C. Hazen #
4

Center for

Environmental

Biotechnology

Tyson et al.,
Nature
(2004)

Community structure and metabolism through reconstruction
of genomes from the environment

Ferroplasma type II

3/18/2013

©T. C. Hazen #
5

Center for

Environmental

Biotechnology

Plane Parts vs. Flying


Completed genomes provide “parts lists” for many
microbes, we still have very little understanding of how
they give rise to living systems.


Knowing the working parts of a 747 jet gives few clues
as to how it flies.


genes, proteins, metabolites, and multimolecular
assemblies (“molecular machines”) interact in an
intricate labyrinth of pathways and networks to create,
sustain, and reproduce the living cell

complexity well
beyond the engineering of a 747.


A systems approach will transform biology from an
empirical and descriptive science to a more
quantitative and predictive science having the potential
to manipulate and use living systems and their
components.

3/18/2013

©T. C. Hazen #
6

Center for

Environmental

Biotechnology

Integration of new science
areas to build a knowledge of
how to fly the plane


Ecogenomics


Phenomics


Transcriptomics


Proteomics


Metabolomics (lipidomics, fluxomics)


Bioinformatics to integrate the pathways
and build the models to understand how
to fly the plane

The Virtual Institute of Microbial
Stress and Survival

U Washington

http://vimss.lbl.gov



High Throughput Comparative Molecular
Environmental Microbiology for
Breakthrough Science and New
applications for Bioremediation &
Natural Attenuation Strategies

Design of Project

Phenotypic Microarray

Omnilog System
-

2000 assays,

50 96
-
well plates at one time

FTIR Profiling


Synchrotron FTIR time course of infrared absorption intensity,
indicative of oxidative stress levels in different biologically
important molecules in
Desulfovibrio vulgaris

after exposure to
atmospheric oxygen.



Also found signatures for Cytochrome B hemes

O
2

Stress in
Desulfovibrio vulgaris

Fischer exact test of GO terms for DE genes as measured by microarrays at
2h revealed numerous up
-
regulated genes in cell wall and polysaccharide
metabolism. Candidates for EPS activity.


Also


why all the sugar activity given D.v. doesn’t use hexoses for cell growth?

nSig
nUarray
p
GOName
26
142
0.0002
transcription termination
4
6
0.0008
4-diphosphocytidyl-2C-methyl-D-erythritol synth
4
6
0.0008
O-acetyltransferase activity
5
11
0.0017
primary active transporter activity
5
11
0.0017
cell wall
11
51
0.0043
proline-tRNA ligase activity
2
2
0.0082
purine base catabolism
2
2
0.0082
adenine catabolism
2
2
0.0082
phenylalanyl-tRNA aminoacylation
2
2
0.0082
prolyl-tRNA aminoacylation
2
2
0.0082
nucleoside triphosphate metabolism
14
77
0.0109
N-acetyltransferase activity
14
77
0.0109
phosphoenolpyruvate-dependent sugar phosph
2
3
0.0233
acyl-CoA or acyl binding
2
3
0.0233
cobalamin [5'-phosphate] synthase activity
2
3
0.0233
chloramphenicol O-acetyltransferase activity
2
3
0.0233
transferase activity, transferring glycosyl groups
2
3
0.0233
transferase activity, transferring hexosyl groups
Comparative genomics pipeline

120 annotated microbial genomes already in pipeline

High quality function
prediction in novel
comparative genome
browser

Operon/regulon
analysis yields
predictions of co
-
regulated genes and
suggests modules of
function

Flagellar control

chemosensing

http://escalante.lbl.gov, username=gtl, password=arkin