Recreating in silico the Natural History of Antibiotic Resistance

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Recreating in silico the Natural History of Antibiotic Resistance. Daniel Barker. Rosanna Alderson. John Mitchell. β -lactamase superfamily. β -lactam hydrolysis. Metallo- β -lactamase classification. T he metallo - β -lactamase superfamily . β -lactamase superfamily. - PowerPoint PPT Presentation

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Recreating in silico the Natural History of Antibiotic Resistance

Daniel BarkerRosanna Alderson

John MitchellBeta lactmases antibiotics summarize1-lactamase superfamilyThe metallo--lactamase superfamily -lactam hydrolysisMetallo--lactamase classification2-lactamase superfamily-lactam hydrolysisMetallo--lactamase classification CATH code 3.60.15.10

Very diverse in range of substrate type.

Overall chemical mechanism for both - lactamases and glyoxalases is hydrolysis catalysed via a metal ion, commonly zinc, that activates a water molecule.

Superfamily also includes the flavoproteins in which a beta-lactamase domain has joined onto a flavodoxin domain.

-lactamase superfamily: An homologous superfamily of evolutionarily related proteins of similar structure, but with functional diversity not all are -lactamases .Classification of domains aligning to flavoprotein.3-lactamase superfamily-lactam hydrolysisMetallo--lactamase classification-lactam

water

substituted -amino acid

ccMoxalactam Hydrolysis(S. maltophilia L1)Spencer, J. et al (2005): scheme 1 4-lactamase superfamily-lactam hydrolysisMetallo--lactamase classificationM0015 1znb (B1)

M0258 1sml (B3)

Stretched- check5-lactamase superfamily-lactam hydrolysisMetallo--lactamase classification

- lactamases

B3B16-lactamase superfamily-lactam hydrolysisMetallo--lactamase classification

subclass B1subclass B2subclass B3- lactamasessubclass B1subclass B2subclass B3The subclasses B1/B2 and B3 should be considered as distinct as the major classes of lactamase e.g. the serine lactamases to reflect their relative diversity in sequence and structure.7Were there two independent evolutionary origins of -lactam hydrolysis in the metallo--lactamase superfamily?Beta lactmases antibiotics summarize8

What was the likely function of the common ancestor of the B1 & B3 subclasses?

Is it likely that lactam hydrolysis evolved independently more than once in this superfamily?9A simplistic analogy 10 what do these people have in common?11

what do these people have in common?12

what do these people have in common?

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what do these people have in common?

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what do these people have in common?

Andy SMITHTerry SMITHAnne SMITH15Going back a number of generations, individuals will share common ancestors 16Warning: the following diagram is purely illustrative. No real family trees were harmed in the making of this diagram.17

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Was this common ancestor a Smith 20

or did the trait Smith originate independently more than once in the same lineage?

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MRCA not a SmithSmith arises independently multiple times23Previous WorkBuilding trees and the Most Recent Common Ancestor (MRCA)approachUnresolved consensus treeBuilding treesMRCA approach24Previous WorkUnresolved consensus treeBuilding treesMRCA approach

11641Independent origins paper clear. Lack of homology Time scalesSpecies tree guide- explain. 25

Previous WorkUnresolved consensus treeBuilding treesMRCA approach

MAFFT- amino acid alignment Estimate parameters for tree building from dataMaximum Likelihood trees built in PhyML

(100 bootstrap replicates WAG+G+I)Orthologous sequences chosen, double no. of each functional class from UniProtKBdatabase Profile aligned against FunTreealignment low gap penaltyExplain evolutionary models 26

Previous WorkUnresolved consensus treeBuilding treesMRCA approachFlavoproteinsB1 lactamasesB2 lactamasesB3 lactamasesGlyoxalasesRibonucleases?We reconstruct the phylogeny 100 times using randomised bootstrap replicatesGroup of proteins with a common function

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Previous WorkUnresolved consensus treeBuilding treesMRCA approachFlavoproteinsB1 lactamasesB2 lactamasesB3 lactamasesGlyoxalasesRibonucleases?If we got an unambiguous tree topology, we could study a single MRCA Group of proteins with a common function

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Previous WorkUnresolved consensus treeBuilding treesMRCA approachFlavoproteinsB1 lactamasesB2 lactamasesB3 lactamasesGlyoxalasesRibonucleases? but the order of branching is not clearly resolvedGroup of proteins with a common function

29Previous WorkUnresolved consensus treeBuilding treesMRCA approach

>1 ----------------------iplp------plsdg--vy-yvwld---------------eftgfgag------------------pltgllv---ypdgri------li----d-----pvcgeggthgllnwg-apg-----klgr-------klkyilithghgdhigglwgllkir--ga-------tvygp------------ggtrallprg--g--------------------------eytlflkggwpdcyy---pga--------------------------------hycd---------rwivwlpeg-rvllg-----------------g---ccfgyrf---avp--gkl-----------------------------------------------------gd--ltlacd-------ftavlvhe-----------y---------------wpktiddyr--sk----fdqvaelg---gvkklipghgd-----------------------------------ggq-----g--lllkayr---dff------------------------------------------------------>2---------------------------------lldg--vy----------------------flgfslg-------------------ry-lwi--yyprgcv------lf----d-----pgcgegtphllkhigfapg-----vigr-------glkyillthghgdhvgglkelleif--ga-------tvygp------------agtaallarg--glmfpy-gl------------------eytlllgrgwpdfyy---plp---------------------------------gcd---------rlihpgpgdtrvflg-----------------d---clfgyhl---dpg--gtl-----------------------------------------------------gd--iclacdp--egirgpdvlcgd----------rc-------f-------wpktle--k--ds----fdkikelpkcdglkcllgghgg----------------------------------ygrq-----glkllirkyr---elf------------------------------------------------------>3 ---------------------------------------iy-yglld---------------gfagfgav-------------------lt-lwv---tpdgli------lf----d-----ggcgdgtphllldwg-vpg-----pigk-------klkyilithghgdhigglgllgcrr--ga-------yvygp------------gggrlllpkg--g--------------------------ddtlllgggwpdfyy---pga--------------------------------hwpd---------rvirwlpeg-rvllg-----------------g---cvftarl---tlg--gtl-----------------------------------------------------gc--ltwpckgldglkpgcdvlvge-----------y-------y-------ypgliddyr--hr----fpqaralp---gclillpghgg-----------------------------------ggq-----g--lllkeyl---ely------------------------------------------------------ASRSo we went back to our 100 bootstrap reconstructed trees Highlight here how we could just code function and logically estimate ancestor- but not very informative. Instead used ASR to get an estimation at a higher granularity.

Using one tree isnt feasible. 30Previous WorkUnresolved consensus treeBuilding treesMRCA approach

>1 ----------------------iplp------plsdg--vy-yvwld---------------eftgfgag------------------pltgllv---ypdgri------li----d-----pvcgeggthgllnwg-apg-----klgr-------klkyilithghgdhigglwgllkir--ga-------tvygp------------ggtrallprg--g--------------------------eytlflkggwpdcyy---pga--------------------------------hycd---------rwivwlpeg-rvllg-----------------g---ccfgyrf---avp--gkl-----------------------------------------------------gd--ltlacd-------ftavlvhe-----------y---------------wpktiddyr--sk----fdqvaelg---gvkklipghgd-----------------------------------ggq-----g--lllkayr---dff------------------------------------------------------>2---------------------------------lldg--vy----------------------flgfslg-------------------ry-lwi--yyprgcv------lf----d-----pgcgegtphllkhigfapg-----vigr-------glkyillthghgdhvgglkelleif--ga-------tvygp------------agtaallarg--glmfpy-gl------------------eytlllgrgwpdfyy---plp---------------------------------gcd---------rlihpgpgdtrvflg-----------------d---clfgyhl---dpg--gtl-----------------------------------------------------gd--iclacdp--egirgpdvlcgd----------rc-------f-------wpktle--k--ds----fdkikelpkcdglkcllgghgg----------------------------------ygrq-----glkllirkyr---elf------------------------------------------------------>3 ---------------------------------------iy-yglld---------------gfagfgav-------------------lt-lwv---tpdgli------lf----d-----ggcgdgtphllldwg-vpg-----pigk-------klkyilithghgdhigglgllgcrr--ga-------yvygp------------gggrlllpkg--g--------------------------ddtlllgggwpdfyy---pga--------------------------------hwpd---------rvirwlpeg-rvllg-----------------g---cvftarl---tlg--gtl-----------------------------------------------------gc--ltwpckgldglkpgcdvlvge-----------y-------y-------ypgliddyr--hr----fpqaralp---gclillpghgg-----------------------------------ggq-----g--lllkeyl---ely------------------------------------------------------ASR and obtained the sequence of the putative MRCA of B1, B2 & B3 in each tree.Highlight here how we could just code function and logically estimate ancestor- but not very informative. Instead used ASR to get an estimation at a higher granularity.

Using one tree isnt feasible. 31Previous WorkUnresolved consensus treeBuilding treesMRCA approach

HSSSFF{H, S}

S{S, F} S{S ,F}

We had reconstructed the sequence probabilistically for each node of the tree for each of our 100 runs. So we had 100 putative MRCA sequences.This is a parsimonious approach- ML makes different evolutionary assumptions not necessarily the route with the fewest changes. Can differentiate between unions based on quantitative probabilities.

Alignment bigger32100 MRCAs47 match IPR00101853 do not match47 of the 100 MRCA sequence predictions hit InterPro signature IPR001018, Beta-lactamase, class-B, conserved site.Previous WorkUnresolved consensus treeBuilding treesMRCA approachMRCA approach33100 MRCAs47 match IPR00101853 do not matchA match to IPR001018, Beta-lactamase, class-B, conserved site, indicates the presence of some key zinc binding and catalytic residues.MRCA approachPrevious WorkUnresolved consensus treeBuilding trees34100 MRCAs47 match IPR00101853 do not matchHowever, it should be considered necessary but not sufficient to