The evolution of the tetrapyrrol biosynthesis resulting in the ..
Recent years saw a dramatic increase in genomics and proteomics data deriving from organisms belonging to all of the three major domains of life. By the way, the use of bioinformatic tools allowed the storage and interpretation of several sources of information (gene structure and organization, gene regulation, protein–protein interactions) and, probably more importantly, their integration, a fundamental step for the global understanding of genomes properties and dynamics. This, in turn, has allowed the emergence of comparative analyses of a huge number of genes and genomes of organisms belonging to taxonomically unrelated groups. All the data gained both from the genomic and the evolutionary studies of different species can be combined together, resulting in a new kind of approach, referred to as phylogenomics.
This novel way of investigating the evolutionary history of genes introduced several advantages, in fact, adopting a genome-scale approach theoretically overcomes incongruence derived from molecular phylogenies based on single genes mainly because (i) non-orthologous comparison (i.e. the comparison of those genes erroneously defined as orthologous) is much more misleading when the analysis is performed on a single gene, whereas it is probably buffered in a multigene analysis and (ii) stochastic error naturally vanishes when more and more genes are considered. Genomics data is a fundamental step for addressing the topic of the evolution of metabolic pathways, and strictly depends on a correct identification of orthologous proteins shared by different genomes.
The identification of orthologs between two genomes often relies on the so-called bidirectional best-hit (BBH) criterion, a reiteration of the algorithm: two proteins, a and b, from genomes A and B respectively, are orthologs if a is the best-hit (i.e. the most similar) of b in genome A and vice versa. For three or more genomes, groups of orthologous sequences can be constructed by extending the relationships with a clustering algorithm. One of the most interesting topic in studying metabolic genes is to explore their organization on the chromosome. In fact, since genes belonging to the same operon are often involved in the same metabolic pathway, it follows that the analysis of gene organization may provide useful hints to disclose the forces driving the assembly and the shaping of a given metabolic route.
Moreover, if an unknown gene is found in operon with genes of a specific process, it might be involved in the same or a related process, especially if this association is evolutionary conserved. The analysis of such genes may provide useful hints in the understanding of the evolution of the complex systems of metabolic interconnections within the cell. In this context, both operon detection and prediction are two of the main phases when facing the issue of the evolution of biosynthetic genes. Although the evolutionary origin of operons and the selective forces promoting or demoting it are still a matter of debate, it is well-established that one of the major benefits of an operon is the co-expression of component genes, leading for example to the co-expression of all the genes that are involved in the same biosynthetic route.
Following and integrating these computational approaches, it is now possible to trace back the evolutionary dynamics of all the genes belonging to a certain metabolic pathway.
Evolution of rosmarinic acid biosynthesis - [PDF …
Tsukatani Y, Yamamoto H, Mizoguchia T, Fujitac Y and Tamiakia H (2013) Completion of biosynthetic pathways for bacteriochlorophyll g in Heliobacterium modesticaldum: The C8‐ethylidene group formation. Biochimica et Biophysica Acta‐Bioenergetics 1827 (10): 1200–1204.
Microorganisms have the potential to adapt to changes in their environment. They may develop novel metabolic functions, via activation of cryptic and silent genes, the selection of mutations in regulatory or structural genes, or by the acquisition of new genes by horizontal transfer.
Extensive studies by Mortlock and his co-workers have shown that under laboratory conditions bacterial catabolic evolution can lead to the use of new sugars and that the development of new catabolic activities is often due to the recruitment of pre-existing enzymes following regulatory mutations. Besides, these experiments have been also performed to demonstrate that the capture of horizontally transferred (xenologous) sequences carried by plasmids of different host ranges can also lead to the accretion of biosynthetic or catabolic abilities.
Indeed, the acquisition of metabolic activities from donor cells to heterologous recipients may have taken place since Archaean times. However, how can the newly acquired genes be brought into the pre-existing regulatory system of the host organism?
It is reasonable to assume that mutational adjustment of pre-existing promoter sequences would take place. This issue can be analyzed under laboratory conditions, by transferring genes for a given metabolic route from a donor organism into a heterologous recipient lacking that pathway, and whose transcriptional apparatus does not recognize the regulatory signals of the donor
It has been reported that under starvation conditions recognition by the host of the transcription signals of the donor can be adjusted to the host transcriptional milieu. There are experimental evidences that when either a promoterless (or harboring transcription promoters not recognized by the host polymerase) cluster of biosynthetic genes (involved in histidine biosynthesis), catabolic genes (Pseudomonas phe genes) or an antibiotic resistance gene (E. coli cam gene) is transferred from a donor bacterium to a heterologous strain initially unable to recognize the transcriptional signal of the donor gene(s), regulatory point mutations occurring under stress conditions can lead to the activation of the donor by the host polymerase on a very short timescale.
In addition to point mutations, the movement of mobile elements, such as transposons, from the host genome to the introgressed plasmid may be responsible for the activation of promoterless genes. Hence, the genetic and molecular analysis showed that, under stress conditions, the transcriptional barriers to the heterologous gene expression were overcome by the occurrence of genetic changes in the donor plasmid, leading to mutated sequences that were efficiently recognized by the host polymerase. By assuming that the processes involved in acquiring new metabolic abilities are comparable to those found in natural populations, it is plausible that during the early stages of cellular evolution entire metabolic pathways might have been spread through the bacterial communities via and adaptation of existing promoters to the new genetic background(s).
Evolution of tetrapyrrole biosynthesis
Gupta RS and Khadka B (2016) Evidence for the presence of key chlorophyll‐biosynthesis‐related proteins in the genus Rubrobacter (phylum Actinobacteria) and its implications for the evolution and origin of photosynthesis. Photosynthesis Research 127 (2): 201–218.
Modulation of chlorophyll biosynthesis by water …
The emergence and refinement of basic biosynthetic pathways allowed primitive organisms to become increasingly less dependent on exogenous sources of amino acids, purines, and other compounds accumulated in the primitive environment as a result of prebiotic syntheses. But how did these metabolic pathways originate and evolve? Then, which is the role that the molecular mechanisms described above (gene elongation, duplication and/or fusion) played in the assembly of metabolic routes? How the major metabolic pathways actually originated is still an open question, but several different theories have been suggested to account for the establishment of metabolic routes All these ideas are based on gene duplication.
Modulation of chlorophyll biosynthesis by water stress in ..
The assimilation of the manganese-calcium complex by the cyanobacteria laid the groundwork for the Cambrian explosion some 2 BY later, and for the evolution of the animal and plant kingdoms that followed .