Origins and Evolution of Bioactive Molecules(Chemical Signalling)

A brief history of antibiotics(co-evolution of antibiotics and their resistance)

?

1940 1950 1960 1970 1980 1990 2000

The Dark Ages(Semmelweis)

Primordial Golden

Pharmacologic

Biochemical GenomicHTS

Target

Disenchantment

(Semmelweis)(again!)

Penicillinasediscovery

Antibiotic resistance plasmids

Increasing Antibiotic Resistance

Transmissiblefluoroquinolone

resistance

FDA Office ofNew Drugs

THE LEAN YEARS

* **

MRSA: UK*, US**Production: 50kg……………………………………………………………………………>106 tons

Side Effects of StreptomycinHeadache

NauseaHearing difficulties, deafness Ringing sensation in the ears

Loss of balanceFatigue

Difficulty in passing urineItchy rashes on the skin

but it cured TB!

Albert Schatz and Selman Waksman Who deserved the Prize?

Fifty years of “Industrial Research” on Antibiotics

EnvironmentalDoubling time:

monthsAeration: low

Nutrients: variableCarbohydrate: limited

Water: variableTemperature: 0-40

pH: 2-10Yield: µgrams

Production

Doubling time: hoursAeration: high

*Nutrients: high and constant

Carbohydrate: highWater: unlimited

Temperature: 25-30pH: 6-7

Yield: grams *Typical substrates for fermentation

Molasses (blackstrap)Fish Meal (herring, anchovy)

Citrus pulpAsparagus juiceCottonseed oil

Malt extractBeef extract Bovine blood

Pork liverDistillers solubles

Hydrolysed rabbit fur

SOME NUMBERS

Number of bacteriophages on Earth 1x1031

Number of bioactive molecules in the Parvome >5x1030

Number of microbes on Earth 5x1030

Number of stars in the Universe 7x1021

Number of humans on Earth 6x109

Number of microbes in all humans 6x1023

Number of human cells in one human 1x1013

Number of microbial cells in one human gut 1x1014

Number of human genes in one human 2.5x104

Number of microbial genes in one human gut 3x106

Combined length of all bacteriophages on Earth 108 Ly

Diameter of the Milky Way 105 Ly

* The US national debt >1x1014

* Number of bubbles in one bottle of Champagne 1x105

(Revised from Kyrpides, 2009)

(Rumbaugh, 2007)

The Parvome

Inter-Kingdom Signalling

Origins and Evolution of Bioactive Small Molecules

• Distribution: universal, ancient• Bioactivities: wide range, concentration-dependence• Receptors: mostly macromolecules (cross-species)• Structures: small number of major classes (with

decoration)• Biosynthesis: frequently “assembly line”• Properties and applications: multitudinous

The Ages of Planet Earth

(bio)Chemical Evolution

Hadean Period

LUCA(Last Universal Common Ancestor)

(Modern) Tree of Life

(RNA World)Ribozymes

Meteorites and primordialreactions

“Specialised” Microbial & Plant

MetabolismPrimary Secondary

The Tree of Life

-2.0

-4.0

-0.1

-1.0

-3.0

Origin of Earth (4.5 Billion years)

Last common ancestor

2.3

1.5

1.0

ProteobacteriaCyanobacteria

PlantsDrosophila

Crenarchaeota Euryarchaeota

Gram positivesMouse

0.1

?

3.8

Anoxic(H2, NH3, CO2,)

Chemical evolution/Prebiotic synthesis of biomolecules

Origin of oxygenicphotosynthesis

Increasing [O2]

in atmosphere

Origin of Metazoans20% [O2]

Cambrian Precambrian

Age of Dinosaurs

Origin of Eukaryotes

Origin of Prokaryotes

2.1

Amitochondriate

Bacteria Eukaryotes Archaea

Aminoglycoside biosynthesis in a streptomycete

MODULAR ASSEMBLY LINESFOR BIOACTIVE COMPOUNDS

Polyketide synthase

Nonribosomal peptide synthase

Tetracycline, rapamycin, erythromycin

Daptomycin, polymixin, vancomycin

Carbonaceous meteoritesas sources of

chemical intermediates Pizzarello & Shock (2010)

Primordial amino acid components of non-ribosomal peptides

β-alanine, α-aminobutyric acid, β-aminobutyric acid, γ-amino-butyric acid, α-amino-isobutyric acid, α,γ-diaminobutyric acid, α,β-diaminopropionic acid, α-hydroxy-γ-aminobutyric acid, isoserine, N-methylalanine, 3-methylglutamic acid, isovaline, norvaline, sarcosine

etc…

Diketopiperazines: potential catalysts and signals

There are at least three mechanisms for the synthesis of DKPs!

Targets (binding sites) of bioactive small molecules and macromolecular evolution

• Transcription (rifampicin, streptolydigin)• Replication (novobiocin)• *Translation (tetracycline, streptomycin,

chloramphenicol)• Cell wall synthesis (penicillin, vancomycin)• Metabolic pathways (azaserine)

Did bioactive small molecule interactions play roles in the evolution of cellular macromolecules such as ribosomes and polymerases?

Antibiotic Binding Sites (Receptors) on Prokaryote Ribosomes

30S 50S

This 2.5 mD macromolecule is the sensor/receptor for many signals.

A model for the chronological evolution of the ribosome basedon accretion from existing structures.

(Note: no interactions with small molecules!)

Harish and Caetano-Anolles (2012)PLoS ONE 7(3): e32776.doi:10.1371/journal.pone.0032776

KEEP CLEANWash your hands!

PNAS 2012,in press.

THE FUTURE!

Analysis of interactive bacterial cell networksWatrous et al 2012.

Microbes maketh man (people are not only people)