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Biosimplicity: Engineering Simple Life
Tom KnightMIT Computer Science andArtificial Intelligence Laboratory
Simplicity is the ultimate sophistication
-- Leonardo da Vinci
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Measuring Complexity
• Number of components• Size of description• Size of functional
model
Have you ever thought... about whatever man builds, that all of man'sindustrial efforts, all his calculations and computations, all thenights spent over working draughts and blueprints, invariablyculminate in the production of a thing whose sole and guidingprinciple is the ultimate principle of simplicity?In any thing at all, perfection is finally attained, not when there isno longer anything to add, but when there is no longer anything totake away. -- Antoine de Sainte Exupery, in "Wind, Sand, and Stars"
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Engineered Simple Organisms• modular• understood• malleable• low complexity
• Start with a simple existing organism• Remove structure until failure• Rationalize the infrastructure• Learn new biology along the way
The chassis and power supply for our computing
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Some history…• Confusion over what PPLO/Mycoplasma were
“The Microbe of pleuorpneumonia” Nocard 1896
• 1932 isolation of “PPLO.” Koch postulates.• 1958 Klieneberger-Nobel identifies them as free
living bacterial species• Morowitz 1962 SciAm: “the smallest living cell”• 1980 Gilbert effort to sequence M. capricolum• 1982 Morowitz “complete understanding of life”• 1996 Fraser et al. M. genitalium sequence• 1999 Hutchison et al. Minimal genome set for
M. genitalium
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Relative Complexity
100 1K 10K 100K 1M 10M 100M 1G 10G 100G
Gen
e
Plas
mid
Myc
opla
sma
geni
taliu
m (5
80 k
B)
Mes
opla
sma
floru
m (7
93 k
B)
E. C
oli (
4.6
MB
)
S. C
erev
isia
e (1
2 M
B)
Hum
an (3
.3 G
B)
Lilly
(12
GB
)
T7 P
hage
(36
kB)
Log Genome Size, base pairs
Alive
Autotroph
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From Giovannoni et al. 2005
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Choosing an organism• Safe
BSL-1 organism -- insect commensal
• Un-regulatedNot a crop plant or domesticated animal
pathogen
• Fast growing40 minute doubling timevs. six hours for M. genitalium
• Convenient to work withFacultative anaerobe
• Small genome• Known sequence• Complete annotation
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The Mollicute Bibliome
Complete collection of mycoplasma related papers:
• 6,418 and counting
• All books and book chapters also
• Endnote & Refworks
• Downloaded .pdfs for articles > 1995
• Scanned articles and books, OCR with Abbyy Finereader
• Plans for a Google appliance search engine
• Collaboration for “shallow semantic” understanding
• people.csail.mit.edu/tk/mfpapers/ user=meso, pass=meso
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Mesoplasma florum
1 u
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Tomographic TEM
CourtesyJensen Lab,Caltech
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Culture Medium 1161
• Beef Heart infusion• 4% Sucrose• Fresh yeast culture broth• 20% horse serum• Penicillin• Phenol red
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Defined mediumSodium phosphateKClMagnesium sulfate
GlycerolSpermine
Nicotinic acidThiamineRiboflavinPyridoxamineThioctic acidCoenzyme A
Amino acids (minus asp, glu)GuanineUracilThymineAdenine
Glucose
BSAPalmitic acidOleic acid
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Synthesis vs. Import
• Mycoplasma import virtually all small biochemical molecules
• Each import is done with a specific membrane protein – some are capable of importing a class
• Complexity is reduced if the import is simpler than the synthesis
• Example of the opposite:Glutamine Glutamic acidAsparagine Aspartic acid
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Sequencing the genome• First sequenced small portions of the
genome to test that we had the correct speciesCompared the results to Genbank entriesSequenced PTS system gene, identical to
reported sequenceSequenced 16S rRNA (unreported)Discovered identical to Mesoplasma
entomophilum 16S rRNA sequence – probably the same species Genbank entry
• Measured genome size with pulse field gels• Sequenced 12% of genome to see what we
were up against
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PFGE of Mesoplasmagenomic DNA
1.2% agarose 9C 6V/cm Ramped 90 - 120 sec 48 hours
yyeast marker
lambda marker
meMesoplasma entomophilum
mfMesoplasma florum
mlMesoplasma lactucae
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I-CeuI digestion
• Special restriction enzymes cut only at 23S rRNA sites
5´ ..TAACTATAACGGTC CTAA^GGTAGCGA..3´
3´ ..ATTGATATTGCCAG^GATT CCATCGCT..5´
Calculate the number of rRNA sites in the genome from the number of cut fragments
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I-CeuI digests
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rRNA sequences
• Degenerate primers
• The two rRNA sequences are different:
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Library creation• Randomly cut genomic DNA with EcoRI• Shotgun cloned into pUC18 vector• Sequenced the inserts (0.1 – 8 Kb)
• Sheared the genomic DNA with a needle• End repaired• Cloned into defective lambda phage vector• Packaged vector into phage heads• Infected E. coli cells with phage
~ 40 Kb inserts
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What we learned from partial sequence
• Almost all “old friends”• Little or no extra junk• Inter-gene sequences small (-4 to 30 bp)• Little transcriptional control• High AT vs. GC content – 27% average GC
20% in typical genes, even less in control regions
40% in rRNA regions
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Origin of Replication
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Whitehead Agreement
• Whitehead agreed in January 2002 to sequence the organism
• Estimated to take about two hours of time on their sequencers“Sure, we can do it Tom, but what do we do with
the rest of the day after the coffee break?”
• “How many other organisms like this are there?”300
• “Why don’t we sequence them all?”• Good draft available November 2002• Gaps closed July 2003 -- final November 2003
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Gap closure• 9 gaps remained• Long range PCR • Primer walking• One difficult sequence
Poly A region 16-17 bp longSequencing stutteredReprime with aaaaaaaaaaaaaaaag
• Repeat region 186 bp in surface lipoproteinGive up on accurate sequence, PCR for length
• Final assembly verification
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Genome characteristics
• 793281 base pairs• 26.52% G + C• 682 protein coding regions
UGA for tryptophanNo CGG codon or corresponding tRNAClassic circular genomeoriC, terminator region, gene orientation
• 39 stable RNAs29 tRNAs2x 16S, 23S, 5SRNAse-P, tmRNA, SRP
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Standard Motifs• -10 present usually very highly conserved
Often preceded by a “TG” 1-2 bp upstream
• Seldom a conserved -35 region• RBS is standard Shine-Dalgarno• Alternate RBS matches complementary
region of 16S rRNA UAACAACAU (Loechel 91)• Standard stem-loop terminators with loop
TTAA6-8 poly T tail in forward direction
• dnaA box TTATCCACA• Four ribo-box sequences (Thi, Ile, Val,
Guanine)
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Understand the metabolism
• Identify major metabolic pathways by finding critical genes coding for known enzymes
• Predict necessary enzymes which may not have been found
• Evaluate the list of unknown function genes for candidates
• Build the major metabolic pathway map of the organism
• Consider elimination of entire pathways
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Mfl214, Mfl187
Mfl516, Mfl527, Mfl187
Mfl500 Mfl669Mfl009, Mfl033,Mfl318, Mfl312
Mfl666, Mfl667, Mfl668
Mfl023, Mfl024,Mfl025, Mfl026
ribose ABC transporter
glucosesucrose trehalose xylose
unknownfructose
sn-glycerol-3-phosphate ABC transporter
Mfl254, Mfl180, Mfl514, Mfl174, Mfl644, Mfl200, Mfl504, Mfl578, Mfl577, Mfl502, Mfl120, Mfl468, Mfl175, Mfl259Mfl039, Mfl040, Mfl041, Mfl042, Mfl043, Mfl044, Mfl596, Mfl281
Glycolysis
Mfl497 Mfl515, Mfl526 Mfl499 Mfl317?, Mfl313? ?
Mfl181
beta-glucoside
Mfl009, Mfl011, Mfl012, Mfl425, Mfl615, Mfl034, Mfl617, Mfl430, Mfl313?
PTS II SystemMfl519, Mfl565
chitin degradation
Mfl223, Mfl640, Mfl642, Mfl105, Mfl349
Pentose-Phosphate Pathway
glyceraldehyde-3-phosphate
Mfl619, Mfl431, Mfl426
Mfl074, Mfl075, Mfl276, Mfl665, Mfl463, Mfl144, Mfl342, Mfl343, Mfl170, Mfl195, Mfl372
Mfl419, Mfl676, Mfl635, Mfl119, Mfl107, Mfl679, Mfl306, Mfl648,Mfl143, Mfl466, Mfl198, Mfl556, Mfl385
Mfl076, Mfl121, Mfl639, Mfl528, Mfl530, Mfl529, Mfl547, Mfl375
Purine/Pyrimidine Salvage
glucose-6-phosphate
ribose-5-phosphate
Mfl413, Mfl658
xanthine/uracilpermease
DNA RNAMfl027, Mfl369
competence/DNA transport
DNA Polymerase
degradation
RNA Polymerase
Mfl047, Mfl048, Mfl475
Mfl237
protein translocation complex (Sec)
protein secretion (ftsY)
srpRNA, Mfl479
Signal Recognition Particle (SRP) Ribosome
Export
Mfl182, Mfl183, Mfl184
Mfl509, Mfl510, Mfl511
Mfl652Mfl557
Mfl605Mfl019
Mfl094, Mfl095, Mfl096, Mfl097,
Mfl098
Mfl015
spermidine/putrescineABC transporter
unknown amino acidABC transporterglutamine
ABC transporter
oligopeptide ABC transporter
arginine/ornithineantiporter lysine
APC transporteralanine/Na+ symporter
glutamate/Na+symporter
Mfl016, Mfl664
putrescine/ornithineAPC transporter
23sRNA, 16sRNA, 5sRNA,
Mfl122, Mfl149, Mfl624, Mfl148, Mfl136, Mfl284, Mfl542, Mfl132, Mfl082,Mfl127, Mfl561, Mfl368.1, Mfl362.1, Mfl129, Mfl586, Mfl140, Mfl080,
Mfl623, Mfl137, Mfl492, Mfl406
Mfl608, Mfl602, Mfl609, Mfl493, Mfl133, Mfl141, Mfl130, Mfl151, Mfl139, Mfl539, Mfl126, Mfl190, Mfl441, Mfl128, Mfl125, Mfl134, Mfl439, Mfl227,
Mfl131, Mfl123, Mfl638, Mfl396, Mfl089, Mfl380, Mfl682.1, Mfl189, Mfl147, Mfl124, Mfl135, Mfl138, Mfl601, Mfl083, Mfl294, Mfl440?
proteins
degradation
Mfl418, Mfl404, Mfl241, Mfl287, Mfl659, Mfl263, Mfl402, Mfl484, Mfl494, Mfl210, tmRNA
tRNA aminoacylation
ribosomal RNA transfer RNA
messenger RNA
Mfl029, Mfl412, Mfl540, Mfl014, Mfl196,Mfl156, Mfl282, Mfl387, Mfl682, Mfl673, Mfl077, rnpRNA
Mfl563, Mfl548, Mfl088, Mfl258, Mfl329, Mfl374, Mfl541, Mfl005, Mfl647, Mfl231, Mfl209
Mfl613, Mfl554, Mfl480, Mfl087, Mfl651, Mfl268, Mfl366, Mfl389, Mfl490, Mfl030, Mfl036, Mfl399, Mfl398, Mfl589,
Mfl017, Mfl476, Mfl177, Mfl192, Mfl587, Mfl355
Mfl086, Mfl162, Mfl163, Mfl161
amino acids
Amino Acid Transport
intraconversion?
Mfl590, Mfl591
Lipid SynthesisMfl230, Mfl382, Mfl286, Mfl663, Mfl465, Mfl626
fatty acid/lipid transporter
Identified Metabolic Pathways in
Mesoplasma florum
Mfl384, Mfl593,Mfl046, Mfl052
L-lactate,acetate
Mfl099, Mfl474,Mfl315, Mfl325,Mfl482
cardiolipin/phospholipids
membrane synthesis
x22
Mfl444, Mfl446, Mfl451
variable surface lipoproteins
hypotheticallipoproteins
phospholipid membrane
Mfl063, Mfl065, Mfl038,Mfl388
Mfl186 formate/nitratetransporter
Mfl060, Mfl167, Mfl383, Mfl250
Formyl-THF Synthesis
THF?
x57hypothetical transmembrane proteins
met-tRNA formylationMfl409, Mfl569
Mfl152, Mfl153, Mfl154
Mfl233, Mfl234, Mfl235
Mfl571, Mfl572
Mfl356, Mfl496, Mfl217
Mfl064, Mfl178Nfl289, Mfl037, Mfl653, Mfl193
Mfl109, Mfl110, Mfl111, Mfl112, Mfl113, Mfl114,
Mfl115, Mfl116
ATP Synthase Complex
ATP ADP
phosphate ABC transporter
phosphonate ABC transporter
metal ion transporter
Mfl583, Mfl288, Mfl002, Mfl678, Mfl675, Mfl582,
Mfl055, Mfl328
Mfl150, Mfl598, Mfl597, Mfl270, Mfl649
acetyl-CoA
cobalt ABC transporter
Mfl165, Mfl166
K+, Na+transporter
Mfl378
malate transporter?
Mfl340, Mfl373, Mfl521, Mfl588
Pyridine Nucleotide Cycling
NAD+
Electron Carrier Pathways
NADHNADPH
NADP
Flavin Synthesis
riboflavin?
FMN, FADMfl283, Mfl334
Mfl193
Mfl057, Mfl068, Mfl142,Mfl090,
Mfl275
Mfl347, Mfl558
G. Fournier02/23/04
x13+
unknown substrate transporters
PRPP
niacin?
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How Simple is this?• Missing cell wall, outer membrane• Missing TCA cycle• Missing amino acid synthesis• Missing fatty acid synthesis• One sigma factor• Small number of dna binding proteins• One insertion sequence, probably not
active• One restriction system (Sau3AI-like)• CTG/CAG methylation (function?)• Evidence for shared protein function
MDH/LDH (Pollack 97 Crit rev microbiol 23:269)
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Minimal is not always simple• Shared function of parts• Overlapped genes• Tradeoff of import vs. synthesis
• Example:Television set designShared deflection coil, high voltage power
supply, isolated filament supplyThree functions, a single circuit, a difficult
engineering, modeling, debugging, and repair task
• how many genes have multiple functions
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DNA Methylation
• Bisulfite conversion of genomic DNA• Sequencing of converted DNA to identify
methylated C positions
• Results: GATC sequences, as expected• Unexpected: CAG and CTG sequences
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Current work• Array experiments
Close species Transcriptional units, pseudo-genes TRASH
• Protein species by LC/LC/MS/MS• Elimination of the restriction system• Plasmid system
pBG7AU based
• Recombination system Positive/negative selection
• Yeast chromosome transfer• Genome edits to reduce size• Genome edits to modularize• Genome edits to eliminate complexity• Use as a construction chassis
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Reconstruct the Genome• Use recombination techniques to edit the
genome• Eliminate unnecessary genes• Remove overlaps• Standardize promoters, ribosomal binding
sites• Identify transcriptional and translational
regulators• Recode proteins to use a reduced portion of
the coding spaceThe code is 4 billion years old,it’s time for a rewrite
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YAC mutagenesis
• Bring up YAC technology Spheroplasts, old YAC plasmid sequencing
• Triple transform with MF chromosome and pRML1 (Spencer 92) pRML2 Genome inactive except for ARS, telomeres, selection
markers
• Use yeast recombination systems for genome editing
• Isolate and recircularize YAC to form a new genome• Lipid encapsulate genome into vesicles• Fuse vesicles with genome-killed wild type cells
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Proteome• Collaboration with Steve Tannenbaum / Yingwu
Wang• 2-D gels + MS spot ID• LC/LC/MS/MS ID of trypsin digests
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Riboswitch Analysis
• Collaboration with Ron Breaker / Adam Roth
• Discovery of unique riboswitches specific for GTP rather than dGTP
• Found in no other sequenced genomes
• Analysis of close relatives under way
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Engineer plasmids• No known plasmids for this class of
organism• Renaudin has made plasmids using the
chromosomal OriC as the replicative elementLartigue 03
• M. mycoides has pADB201 and pBG7AU rolling circle plasmids similar to pE194 (1082 bp)
• We know the antibiotic sensitivities and have working resistance genes
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Kit Part the genome
• Make Biobrick parts from each gene, tRNA, promoter, other part-like genome element
• Attempt to develop techniques for recombining parts into coherent modules
• Develop techniques for assembling and modeling the resulting structures
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Thanks to…• Harold Morowitz• Greg Fournier• Gail Gasparich• Bob Whitcomb• Eric Lander• Bruce Birren• Nicole Stange-
Thomann• George Church• Roger Brent• Grant Jensen• Yingwu Wang
• Nick Papadakis• Ron Weiss• Drew Endy• Randy Rettberg• Austin Che• Reshma Shetty• MIT Synthetic biology
working group• DARPA, NTT, NSF,
Microsoft
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Synthetic Biology
• An alternative to understanding complexity is to remove it
• This complements rather than replaces standard approaches
• Engineering synthetic constructs will be easierEnabling quicker more facile experimentsEnabling deeper understanding of the basic
mechanismsEnabling applications in nanotechnology,
medicine and agricultureSimplicity is the ultimate sophistication
-- Leonardo da Vinci