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  Topic: Evolution of multiple-parts-required pathways, Lit on this< Next Oldest | Next Newest >  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: July 14 2003,00:30   

From:
http://www.arn.org/boards/ubb-get_topic-f-13-t-000803.html

Whoa, Nelson just admitted that multiple-parts required systems can evolve rapidly by cooption of parts.  Which is what we've been arguing all along:

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Another great example of this might be the 2,4 DNT pathway. The first operon is taken from the naphthalene degradation pathway, the second operon is taken from distantly related chlorophenol and nitrophenol pathways. There are others but finding out where they came from would just be a guess. However, it shows just how bacteria when faced with something completely new have the tools to construct something just as new in order to overcome the challenge.
It looks like this paper may have convinced him that IC isn't all its cracked up to be:

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J Bacteriol. 2002 Aug;184(15):4219-32.

Erratum in:
J Bacteriol 2002 Nov;184(21):6084.
 
Origins of the 2,4-dinitrotoluene pathway.

Johnson GR, Jain RK, Spain JC.

Air Force Research Laboratory, U.S. Air Force, Tyndall Air Force Base, Florida 32403, USA.

The degradation of synthetic compounds requires bacteria to recruit and adapt enzymes from pathways for naturally occurring compounds. Previous work defined the steps in 2,4-dinitrotoluene (2,4-DNT) metabolism through the ring fission reaction. The results presented here characterize subsequent steps in the pathway that yield the central metabolic intermediates pyruvate and propionyl coenzyme A (CoA). The genes encoding the degradative pathway were identified within a 27-kb region of DNA cloned from Burkholderia cepacia R34, a strain that grows using 2,4-DNT as a sole carbon, energy, and nitrogen source. Genes for the lower pathway in 2,4-DNT degradation were found downstream from dntD, the gene encoding the extradiol ring fission enzyme of the pathway. The region includes genes encoding a CoA-dependent methylmalonate semialdehyde dehydrogenase (dntE), a putative NADH-dependent dehydrogenase (ORF13), and a bifunctional isomerase/hydrolase (dntG). Results from analysis of the gene sequence, reverse transcriptase PCR, and enzyme assays indicated that dntD dntE ORF13 dntG composes an operon that encodes the lower pathway. Additional genes that were uncovered encode the 2,4-DNT dioxygenase (dntAaAbAcAd), methylnitrocatechol monooxygenase (dntB), a putative LysR-type transcriptional (ORF12) regulator, an intradiol ring cleavage enzyme (ORF3), a maleylacetate reductase (ORF10), a complete ABC transport complex (ORF5 to ORF8), a putative methyl-accepting chemoreceptor protein (ORF11), and remnants from two transposable elements. Some of the additional gene products might play as-yet-undefined roles in 2,4-DNT degradation; others appear to remain from recruitment of the neighboring genes. The presence of the transposon remnants and vestigial genes suggests that the pathway for 2,4-DNT degradation evolved relatively recently because the extraneous elements have not been eliminated from the region.
Or perhaps it was this more recent one that just turned up in 'related articles':

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Appl Microbiol Biotechnol. 2003 May 15 [Epub ahead of print].  
 
Evolution of catabolic pathways for synthetic compounds: bacterial pathways for degradation of 2,4-dinitrotoluene and nitrobenzene.

Johnson GR, Spain JC.

Air Force Research Laboratory, United States Air Force, FL 32403, Tyndall Air Force Base, USA.

The pathways for 2,4-dinitrotoluene (2,4-DNT) and nitrobenzene offer fine illustrations of how the ability to assimilate new carbon sources evolves in bacteria. Studies of the degradation pathways provide insight about two principal strategies for overcoming the metabolic block imposed by nitro- substituents on aromatic compounds. The 2,4-DNT pathway uses novel oxygenases for oxidative denitration and subsequent ring-fission. The nitrobenzene pathway links facile reduction of the nitro- substituent, a novel mutase enzyme, and a conserved operon encoding aminophenol degradation for mineralization of nitrobenzene. Molecular genetic analysis with comparative biochemistry reveals how the pathways were assembled in response to the recent appearance of the two synthetic chemicals in the biosphere.
Imagine that, bacteria naturally evolving ways to break down human-designed chemicals they've never seen before...



Additional articles:

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Curr Opin Biotechnol. 2003 Jun;14(3):262-9.  
 
The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds.

Top EM, Springael D.

Department of Biological Sciences, 347 Life Sciences Building South, University of Idaho, 83844-3051, Moscow ID, USA

Retrospective studies clearly indicate that mobile genetic elements (MGEs) play a major role in the in situ spread and even de novo construction of catabolic pathways in bacteria, allowing bacterial communities to rapidly adapt to new xenobiotics. The construction of novel pathways seems to occur by an assembly process that involves horizontal gene transfer: different appropriate genes or gene modules that encode different parts of the novel pathway are recruited from phylogenetically related or distant hosts into one single host. Direct evidence for the importance of catabolic MGEs in bacterial adaptation to xenobiotics stems from observed correlations between catabolic gene transfer and accelerated biodegradation in several habitats and from studies that monitor catabolic MGEs in polluted sites.


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Trends Biochem Sci. 2003 Jun;28(6):336-41.

Metabolites: a helping hand for pathway evolution?

Schmidt S, Sunyaev S, Bork P, Dandekar T.

European Molecular Biology Laboratory Heidelberg, Postfach 102209, D-69012, Heidelberg, Germany

The evolution of enzymes and pathways is under debate. Recent studies show that recruitment of single enzymes from different pathways could be the driving force for pathway evolution. Other mechanisms of evolution, such as pathway duplication, enzyme specialization, de novo invention of pathways or retro-evolution of pathways, appear to be less abundant. Twenty percent of enzyme superfamilies are quite variable, not only in changing reaction chemistry or metabolite type but in changing both at the same time. These variable superfamilies account for nearly half of all known reactions. The most frequently occurring metabolites provide a helping hand for such changes because they can be accommodated by many enzyme superfamilies. Thus, a picture is emerging in which new pathways are evolving from central metabolites by preference, thereby keeping the overall topology of the metabolic network.

  
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