Multifunctional enzymes and evolution of biosynthetic pathways: retro-evolution by jumps

Exploring mitochondrial evolution and metabolism organization principles by comparative analysis of metabolic networks

The endosymbiotic theory proposed that mitochondrial genomes are derived from an alpha-proteobacterium-like endosymbiont, which was concluded from sequence analysis. We rebuilt the metabolic networks of mitochondria and 22 relative species, and studied the evolution of mitochondrial metabolism at the level of enzyme content and network topology. Our phylogenetic results based on network alignment and motif identification supported the endosymbiotic theory from the point of view of systems biology for the first time. It was found that the mitochondrial metabolic network were much more compact than the relative species, probably related to the higher efficiency of oxidative phosphorylation of the specialized organelle, and the network is highly clustered around the TCA cycle. Moreover, the mitochondrial metabolic network exhibited high functional specificity to the modules. This work provided insight to the understanding of mitochondria evolution, and the organization principle of mitochondrial metabolic network at the network level.

Adaptive evolution of mammalian aromatases: lessons from Suiformes

Estrogen synthesis evolved in chordates to control reproduction. The terminal enzyme in the cascade directly responsible for estrogen synthesis is aromatase cytochrome P450 (P450arom) encoded by the CYP19 gene. Mammals typically have a single CYP19 gene but pigs, peccaries and other Suiformes have two or more resulting from duplication in a common ancestor. Duplication of CYP genes in the steroid synthetic cascade has occurred for only one other enzyme, also terminal, 11beta-hydroxylase P450 (P450c11). P450arom and P450c11 share common substrates and even physiological functions as possible remnants from a common P450 progenitor, perhaps an ancestral P450arom, which is supported by phylogenetic analysis. Conserved tissue-specific expression patterns of P450arom paralogs in placenta and gonads of pigs and peccaries suggest how functional adaptation may have proceeded divergently and influenced adopted reproductive strategies including ovulation rate and litter size. Data suggest that the porcine placental paralog evolved catalytically to protect female conceptuses from testosterone produced by male siblings; the gonadal paralog to synthesize a novel, nonaromatizable testosterone metabolite (1OH-testosterone) that may increase ovulation rate. This would represent a coevolution facilitating litter bearing as pigs diverged from peccaries. Evidence of convergence between the peccary CYP19 genes and lower tissue expression may therefore represent initiation of loss of the functional paralogs. Studies on the Suiforme aromatases provide insights into the evolution of the steroidogenic cascade and metabolic pathways in general, how it translates into physiological adaptations (altered reproductive strategies for instance), and how duplicated genes become stabilized or disappear from genomes.

Identification of a novel self-sufficient styrene monooxygenase from Rhodococcus opacus 1CP

Sequence analysis of a 9-kb genomic fragment of the actinobacterium Rhodococcus opacus 1CP led to identification of an open reading frame encoding a novel fusion protein, StyA2B, with a putative function in styrene metabolism via styrene oxide and phenylacetic acid. Gene cluster analysis indicated that the highly related fusion proteins of Nocardia farcinica IFM10152 and Arthrobacter aurescens TC1 are involved in a similar physiological process. Whereas 413 amino acids of the N terminus of StyA2B are highly similar to those of the oxygenases of two-component styrene monooxygenases (SMOs) from pseudomonads, the residual 160 amino acids of the C terminus show significant homology to the flavin reductases of these systems. Cloning and functional expression of His(10)-StyA2B revealed for the first time that the fusion protein does in fact catalyze two separate reactions. Strictly NADH-dependent reduction of flavins and highly enantioselective oxygenation of styrene to (S)-styrene oxide were shown. Inhibition studies and photometric analysis of recombinant StyA2B indicated the absence of tightly bound heme and flavin cofactors in this self-sufficient monooxygenase. StyA2B oxygenates a spectrum of aromatic compounds similar to those of two-component SMOs. However, the specific activities of the flavin-reducing and styrene-oxidizing functions of StyA2B are one to two orders of magnitude lower than those of StyA/StyB from Pseudomonas sp. strain VLB120.

An introduction to metabolic networks and their structural analysis

There has been a renewed interest for metabolism in the computational biology community, leading to an avalanche of papers coming from methodological network analysis as well as experimental and theoretical biology. This paper is meant to serve as an initial guide for both the biologists interested in formal approaches and the mathematicians or computer scientists wishing to inject more realism into their models. The paper is focused on the structural aspects of metabolism only. The literature is vast enough already, and the thread through it difficult to follow even for the more experienced worker in the field. We explain methods for acquiring data and reconstructing metabolic networks, and review the various models that have been used for their structural analysis. Several concepts such as modularity are introduced, as are the controversies that have beset the field these past few years, for instance, on whether metabolic networks are small-world or scale-free, and on which model better explains the evolution of metabolism. Clarifying the work that has been done also helps in identifying open questions and in proposing relevant future directions in the field, which we do along the paper and in the conclusion.

Seeing double: gene duplication and diversification in plant secondary metabolism

Gene duplications drive the recruitment of genes for secondary metabolism. Gene copies are gradually modified to create genes with specificities and expression patterns adapted to the needs of the new pathway in which they are involved. Duplicated genes are often in tandem repeats, forming clusters within the plant genome. However, in some cases, clusters of nonhomologous genes have also been identified as forming a functional unit. The selective forces that have caused the establishment of new pathways are far from understood and might have changed repeatedly during evolution owing to the continuously changing environment. Recent data show that the way several classes of secondary compounds are scattered among species is attributable to independent recruitment and the inactivation of biosynthetic enzymes.

Metabolic interdependence of obligate intracellular bacteria and their insect hosts

Mutualistic associations of obligate intracellular bacteria and insects have attracted much interest in the past few years due to the evolutionary consequences for their genome structure. However, much less attention has been paid to the metabolic ramifications for these endosymbiotic microorganisms, which have to compete with but also to adapt to another metabolism--that of the host cell. This review attempts to provide insights into the complex physiological interactions and the evolution of metabolic pathways of several mutualistic bacteria of aphids, ants, and tsetse flies and their insect hosts.

Paralogues of porcine aromatase cytochrome P450: a novel hydroxylase activity is associated with the survival of a duplicated gene

The gonadal and placental paralogues of porcine aromatase cytochrome P450 (P450arom) were examined for novel catalytic properties to shed light on the evolutionary survival of duplicated copies of an enzyme critical to reproduction. Recombinant gonadal P450arom catalyzed the formation of a novel metabolite from testosterone, identified by gas chromatography/mass spectrometry and biochemical analyses as 1 beta-hydroxytestosterone (1 beta OH-T), in almost equal proportion to 17beta-estradiol (E(2)). This activity was absent in reactions with the porcine placental paralogue (or other orthologues) of P450arom and was minimal with androstenedione. Incubations with both porcine enzymes and with bovine and human P450arom demonstrated that 1 beta OH-T was not aromatizable, and 1 beta OH-T activated the androgen receptor of prostate cancer cells in vitro. Porcine testicular and follicular granulosa tissues synthesized 1 beta OH-T, which was also detected in testicular venous plasma. These results constitute the first of identification of a novel, perhaps potent, nonaromatizable metabolite of testosterone, whose synthesis (paradoxically) can be definitively ascribed to the activity of the gonadal paralogue of porcine P450arom. It probably represents an evolutionary gain of function associated with fixation and the survival of the genes after CYP19 duplication. Novel activities and adaptive functions may exist among other duplicated vertebrate aromatases.

Metabolites: a helping hand for pathway evolution?

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.

Metabolome diversity: too few genes, too many metabolites?

The multitude of metabolites found in living organisms and the calculated, unexpected small number of genes identified during genome sequencing projects discomfit biologists. Several processes on the transcription and translation level lead to the formation of isoenzymes and can therefore explain at least parts of this surprising result. However, poor enzyme specificity may also contribute to metabolome diversity. In former studies, when enzymes were isolated from natural sources, impure protein preparations were hold responsible for broad enzyme specificity. Nowadays, highly purified enzymes are available by molecular biological methods such as heterologous expression in host organisms and they can be thoroughly analyzed. During biochemical analysis of heterologously expressed enzymes poor specificity was observed for enzymes involved in fruit ripening, e.g. in flavour and color formation. Surprisingly broad specificity was shown for the reactants in the case of alcohol acyl-CoA transferase, O-methyltransferase, glucosyltransferase, P450 monooxygenases as well as polyketide synthases and for the product in the case of monoterpene synthases. Literature data confirm the assumption of limited specificity for enzymes involved in metabolism and bioformation of secondary metabolites. It is concluded that metabolome diversity is caused by low enzyme specificity but availability of suitable substrates due to compartmentation has also taken into account.

Disruption analysis of DR1420 and/or DR1758 in the extremely radioresistant bacterium Deinococcus radiodurans

The extremely radioresistant bacterium Deinococcus radiodurans encodes two genes that are homologous to those involved in bacterial lysine biosynthesis. In lysine biosynthesis, these genes are involved in the aminoadipate pathway and the diaminopimelate (DAP) pathway. DR1420 is homologous to lysZ, which is essential for bacterial lysine biosynthesis via the aminoadipate pathway, and DR1758 is homologous to lysA, which is essential for lysine biosynthesis via the DAP pathway. In this study, DR1420 and/or DR1758 were disrupted. Each disruptant of DR1420 and DR1758, and of DR1420 or DR1758 grew in a minimal medium, as did the wild-type. These results show that D. radiodurans performs lysine biosynthesis in a unique way.

Divergent evolution of (betaalpha)8-barrel enzymes

The (betaalpha)8-barrel is the most versatile and most frequently encountered fold among enzymes. It is an interesting question how the contemporary (betaalpha)8-barrels are evolutionarily related and by which mechanisms they evolved from more simple precursors. Comprehensive comparisons of amino acid sequences and three-dimensional structures suggest that a large fraction of the known (betaalpha)8-barrels have divergently evolved from a common ancestor. The mutational interconversion of enzymatic activities of several (betaalpha)8-barrels further supports their common evolutionary origin. Moreover, the high structural similarity between the N- and C-terminal (betaalpha)4 units of two (betaalpha)8-barrel enzymes from histidine biosynthesis indicates that the contemporary proteins evolved by tandem duplication and fusion of the gene of an ancestral 'half-barrel' precursor. In support of this hypothesis, recombinantly produced 'half-barrels' were shown to be folded, dimeric proteins.

Divergence of function in sequence-related groups of Escherichia coli proteins

The most prominent mechanism of molecular evolution is believed to have been duplication and divergence of genes. Proteins that belong to sequence-related groups in any one organism are candidates to have emerged from such a process and to share a common ancestor. Groups of proteins in Escherichia coli having sequence similarity are mostly composed of proteins with closely related function, but some groups comprise proteins with unrelated functions. In order to understand how function can change while sequences remain similar, we have examined some of these groups in detail. The enzymes analyzed in this work include representatives of amidotransferases, phosphotransferases, decarboxylases, and others. Most sequence-related groups contain enzymes that are in the same classes of Enzyme Commission (EC) numbers. We have concentrated on groups that are heterogeneous in that respect, and also on groups containing more than one enzyme of any pathway. We find that although the EC number may differ, the reaction chemistry of these sequence-related proteins is the same or very similar. Some of these families illustrate how diversification has taken place in evolution, using common features of either reaction chemistry or ligand specificity, or both, to create catalysts for different kinds of biochemical reactions. This information has relevance to the area of functional genomics in which the activities of gene products of unknown reading frames are attributed by analogy to the functions of sequence-related proteins of known function.

Phylogeny of related functions: the case of polyamine biosynthetic enzymes

Genome annotation requires explicit identification of gene function. This task frequently uses protein sequence alignments with examples having a known function. Genetic drift, co-evolution of subunits in protein complexes and a variety of other constraints interfere with the relevance of alignments. Using a specific class of proteins, it is shown that a simple data analysis approach can help solve some of the problems posed. The origin of ureohydrolases has been explored by comparing sequence similarity trees, maximizing amino acid alignment conservation. The trees separate agmatinases from arginases but suggest the presence of unknown biases responsible for unexpected positions of some enzymes. Using factorial correspondence analysis, a distance tree between sequences was established, comparing regions with gaps in the alignments. The gap tree gives a consistent picture of functional kinship, perhaps reflecting some aspects of phylogeny, with a clear domain of enzymes encoding two types of ureohydrolases (agmatinases and arginases) and activities related to, but different from ureohydrolases. Several annotated genes appeared to correspond to a wrong assignment if the trees were significant. They were cloned and their products expressed and identified biochemically. This substantiated the validity of the gap tree. Its organization suggests a very ancient origin of ureohydrolases. Some enzymes of eukaryotic origin are spread throughout the arginase part of the trees: they might have been derived from the genes found in the early symbiotic bacteria that became the organelles. They were transferred to the nucleus when symbiotic genes had to escape Muller's ratchet. This work also shows that arginases and agmatinases share the same two manganese-ion-binding sites and exhibit only subtle differences that can be accounted for knowing the three-dimensional structure of arginases. In the absence of explicit biochemical data, extreme caution is needed when annotating genes having similarities to ureohydrolases.