What is an integron?

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José Francisco Toro Lozano
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1 Transferencia Lateral (Horizontal) de Genes y su Impacto en la Diversidad Bacteriana Carlos M. Rodríguez Minguela, Ph.D. Departamento de Biología cmrodriguez@uprm.edu Ext What is an integron? bacterial gene capture and expression system may encode traits that confer selective advantages these may include but are not limited to: 1.antibiotic resistance 3.metabolic genes 2.virulence factors 4.restriction enzymes 1

bacterial gene capture and expression system may encode traits that confer selective advantages these may

2 Structure and function of integrons integrase P(int) 59-be 59-be 59-be 59-be mrna polycistronic P(c) trimethoprim resistant dihydrofolate reductase aminoglycoside modifying enzyme beta-lactamase Function of integrons: excision of captured genes integrase P(int) 2

dihydrofolate reductase aminoglycoside modifying enzyme

3 Function of integrons: exchange of captured genes among different integron classes integrase P(int) Function of integrons: reassortment of captured genes integrase P(int) 3

4 Function of integrons as reservoirs of cryptic genes P(int) imperfect palindromes (2 o structure) 59-be 59-be 59-be 59-be truncated mrna P(c) not expressed could be transferred trimethoprim resistant dihydrofolate reductase aminoglycoside modifying enzyme beta-lactamase Function of integrons as sources of species genome diversity E. coli cell A E. coli cell B integron absent Inactivaton of Intl gene: prevents insertion, rearrangement, and exicision of genes results in the fixation of captured genes 4

enzyme beta-lactamase Function of integrons as sources of species genome diversity E. coli cell A E.

5 Classification of integrons Two major groups: 1. Mobile integrons (resistance integrons): prevalent in clinical strains may confer resistance against 9 different antibiotics physically linked to mobile DNA elements: 1.transposons 2.conjugative transposons 3.conjugative plasmids 5

strains may confer resistance against 9 different antibiotics

6 Two major groups: 2. Superintegrons (chromosomal integrons): large numbers of inserted gene cassettes not associated with mobile DNA elements All integrons are grouped into classes according to the ID% of the integrase amino acid sequence. Classic resistance (mobile) integrons) Class % a.a. ID Class % a.a. ID a.a.=amino acid Class 3 5 intl3 attl3 bla iimp-1 attlc? 3 6

with mobile DNA elements All integrons are grouped into classes according to the ID% of the

7 - Integrons are not mobile by themselves. - they are mobilized by transposons and conjugative plasmids. Secuencias de Inserción y Transposones - elementos genéticos que se mueven de una molécula de DNA a otra -pueden moverse de un lugar a otro en un cromosoma o de un cromosoma a un plásmido 7

Secuencias de Inserción y Transposones - elementos genéticos que se

8 Secuencias de Inserción y Trasnposones Secuencias de inserción transposón más simple p: gen de transposasa reconoce corta y liga DNA durante transposición : inverted repeats, punto de contacto de la transposasa Transposones se componen de dos secuencias de inserción poseen genes adicionales a la p (transposasa) Transposición p p p 8

inverted repeats, punto de contacto de la transposasa Transposones se componen de

9 Horizontal Gene Transfer of Antibiotic Resistance Traits Donor DNA IS element p Donor DNA Donor DNA IS element p Donor DNA Transposons: segments of DNA capable of jumping from one DNA molecule into another, or of moving around to different positions in the genome of a single cell. transposase Target DNA Transposition p Target DNA integron ABR gene integron ABR gene Target DNA Transposition p Target DNA IS = Insertion Sequence (insertion elements are the smallest transposons, they combine to form composite transposons) Composite transposon p = transposase, transposon encoded enzyme that excises the transposon from a donor DNA molecule and inserts it into a recipient DNA molecule Donor DNA Transposase p integron ABR gene p Donor DNA = inverted repeat, identical DNA sequences reading in opposite directions (DNA is double stranded) these are targeted by the transposase and are compatible with the recipient DNA region Transposition into new target DNA (plasmid, chromosomal) Bacteriophage Plasmid Transposon Plasmid Chromosome Chromosome Free DNA 9

transposase Target DNA Transposition p Target DNA integron ABR gene integron ABR gene Target DNA Transposition p Target DNA IS = Insertion Sequence (insertion elements are the smallest transposons,

65% de las diferencias genéticas entre los genomas completos de 70 bacterias relacionadas se debieron a la presencia de elementos genéticos transmitidos

10 65% de las diferencias genéticas entre los genomas completos de 70 bacterias relacionadas se debieron a la presencia de elementos genéticos transmitidos lateralmente genomas de bacteriofagos insertados transposones secuencias de inserción Published articles using next generation high throughput sequencing technology 10

lateralmente genomas de bacteriofagos insertados transposones secuencias de

Nature 437, 376-380 (15 September 2005) novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99%

sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.

11 Nature 437, (15 September 2005) novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run 100-fold increase in throughput over current Sanger sequencing technology shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine Beijing Genomics Institute - reversible terminator-based sequencing chemistry 600 Mb/day, using as little as 100 ng to 1ug starting material 11

12 ABI-SOLiD DNA sequencing by ligation. Output: 6 gigabases of mappable data. Como pueden identificarse genes que han sido transferidos horizontalmente? 12

13 Como pueden identificarse genes que han sido transferidos horizontalmente? Bioinformática: análisis computacional de secuencias de DNA y proteínas análisis comparativo de genomas Como pueden identificarse genes que han sido transferidos horizontalmente? Observaciones que Sugieren Transferencia Lateral de Genes características atípicas en la secuencia de un gen en relación con el resto del genoma. G+C % tendencias en el uso de codones presencia de secuencias repetitivas flanqueando el gen sospechoso 13

Sugieren Transferencia Lateral de Genes características atípicas en la secuencia de un gen en relación con el resto del genoma.

14 Como pueden identificarse genes que han sido transferidos horizontalmente? 2. características atípicas en la secuencia de un gen en relación con el resto del genoma (diferencias en G+C % ) = 65% G+C = 48% G+C Como pueden identificarse genes que han sido transferidos horizontalmente? características atípicas en la secuencia de un gen en relación con el resto del genoma (tendencias diferentes en el uso de codones ) = 65% G+C Pro = CCG Arg = CGT = 48% G+C Pro = CCT Arg = AGA 14

G+C = 48% G+C Como pueden identificarse genes que han sido transferidos horizontalmente?

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Transferencia Lateral (Horizontal) de Genes y su Impacto en la Diversidad Bacteriana

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