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Distinctive Genome Reduction Rates Revealed by Genomic Analyses of Two Coxiella-Like Endosymbionts in Ticks.

Gottlieb Y, Lalzar I, Klasson L - Genome Biol Evol (2015)

Bottom Line: Genome reduction is a hallmark of symbiotic genomes, and the rate and patterns of gene loss associated with this process have been investigated in several different symbiotic systems.However, in long-term host-associated coevolving symbiont clades, the genome size differences between strains are normally quite small and hence patterns of large-scale genome reduction can only be inferred from distant relatives.The CRt genome is an extreme example of a symbiont genome caught in the act of genome reduction, and the comparison between CLEAA and CRt indicates that losses of particular genes early on in this process can potentially greatly influence the speed of this process.

View Article: PubMed Central - PubMed

Affiliation: Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.

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Biosynthetic pathways for B vitamins (A) and cofactors (B) in CRt. Gene names are indicated in colored rectangles. White rectangles indicate pseudogenes. White rectangles with red X indicate a missing gene.
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evv108-F3: Biosynthetic pathways for B vitamins (A) and cofactors (B) in CRt. Gene names are indicated in colored rectangles. White rectangles indicate pseudogenes. White rectangles with red X indicate a missing gene.

Mentions: Genes involved in the production of seven B vitamins are found in the CRt genome (fig. 3), but the completeness of the various pathways varies greatly. The pathways for the synthesis of biotin (B7) and riboflavin (B2), and the cofactors CoA, FMN and FAD are completely retained, as also seen in the genomes of a number of other symbionts of blood-feeding arthropods (Akman et al. 2002; Dunning Hotopp et al. 2006; Nikoh et al. 2014). The pathways for biosynthesis of pyridoxine (B6), folic acid (B9), and pantothenic acid (B5) are each missing a single gene (epd, phoA, and panE, respectively; fig. 3). As seen for the pyridoxine biosynthesis in other species such as Bacillus stearothermophilus and Escherichia coli(Yang et al. 1998), it is possible that the function encoded by epd is instead performed by GapA or another noncanonical enzyme hence yielding a complete pathway in CRt. Similarly for the folate biosynthesis, the function encoded by phoA might be performed by FolE as suggested for Wigglesworthia (Akman et al. 2002) or PhoA may not be required at all (Bermingham and Derrick 2002). For the biosynthetic pathway of pantothenic acid (B5), it was recently shown in Francisella tularensis that the gene panG could substitute the function encoded by panE (Miller et al. 2013). As an ortholog of panG is present in CRt, it might be able to synthesize vitamin B5 by the use of this gene. The biosynthetic pathways for these five B vitamins are identical between the two tick symbionts CRt and CLEAA. In contrast, the two pathways for the synthesis of thiamine (B1) and nicotinate (B3) are both highly degraded in CRt (fig. 3), whereas CLEAA has retained functional copies of all the pseudogenized genes in CRt. However, whereas the CRt genome contains a putative nicotinamide riboside transporter that might provide CRt with the precursor for B3 and NAD(P) from the host, this transporter has been lost in the CLEAA genome and thus retention of the full pathway might be necessary. Additionally, although CLEAA has retained all genes for thiamine biosynthesis that are degraded in CRt, it has lost the gene thiL performing the final step in converting thiamine phosphate to thiamine diphosphate, the form used as cofactor in many enzymes (Begley et al. 1999).Fig. 3.—


Distinctive Genome Reduction Rates Revealed by Genomic Analyses of Two Coxiella-Like Endosymbionts in Ticks.

Gottlieb Y, Lalzar I, Klasson L - Genome Biol Evol (2015)

Biosynthetic pathways for B vitamins (A) and cofactors (B) in CRt. Gene names are indicated in colored rectangles. White rectangles indicate pseudogenes. White rectangles with red X indicate a missing gene.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494066&req=5

evv108-F3: Biosynthetic pathways for B vitamins (A) and cofactors (B) in CRt. Gene names are indicated in colored rectangles. White rectangles indicate pseudogenes. White rectangles with red X indicate a missing gene.
Mentions: Genes involved in the production of seven B vitamins are found in the CRt genome (fig. 3), but the completeness of the various pathways varies greatly. The pathways for the synthesis of biotin (B7) and riboflavin (B2), and the cofactors CoA, FMN and FAD are completely retained, as also seen in the genomes of a number of other symbionts of blood-feeding arthropods (Akman et al. 2002; Dunning Hotopp et al. 2006; Nikoh et al. 2014). The pathways for biosynthesis of pyridoxine (B6), folic acid (B9), and pantothenic acid (B5) are each missing a single gene (epd, phoA, and panE, respectively; fig. 3). As seen for the pyridoxine biosynthesis in other species such as Bacillus stearothermophilus and Escherichia coli(Yang et al. 1998), it is possible that the function encoded by epd is instead performed by GapA or another noncanonical enzyme hence yielding a complete pathway in CRt. Similarly for the folate biosynthesis, the function encoded by phoA might be performed by FolE as suggested for Wigglesworthia (Akman et al. 2002) or PhoA may not be required at all (Bermingham and Derrick 2002). For the biosynthetic pathway of pantothenic acid (B5), it was recently shown in Francisella tularensis that the gene panG could substitute the function encoded by panE (Miller et al. 2013). As an ortholog of panG is present in CRt, it might be able to synthesize vitamin B5 by the use of this gene. The biosynthetic pathways for these five B vitamins are identical between the two tick symbionts CRt and CLEAA. In contrast, the two pathways for the synthesis of thiamine (B1) and nicotinate (B3) are both highly degraded in CRt (fig. 3), whereas CLEAA has retained functional copies of all the pseudogenized genes in CRt. However, whereas the CRt genome contains a putative nicotinamide riboside transporter that might provide CRt with the precursor for B3 and NAD(P) from the host, this transporter has been lost in the CLEAA genome and thus retention of the full pathway might be necessary. Additionally, although CLEAA has retained all genes for thiamine biosynthesis that are degraded in CRt, it has lost the gene thiL performing the final step in converting thiamine phosphate to thiamine diphosphate, the form used as cofactor in many enzymes (Begley et al. 1999).Fig. 3.—

Bottom Line: Genome reduction is a hallmark of symbiotic genomes, and the rate and patterns of gene loss associated with this process have been investigated in several different symbiotic systems.However, in long-term host-associated coevolving symbiont clades, the genome size differences between strains are normally quite small and hence patterns of large-scale genome reduction can only be inferred from distant relatives.The CRt genome is an extreme example of a symbiont genome caught in the act of genome reduction, and the comparison between CLEAA and CRt indicates that losses of particular genes early on in this process can potentially greatly influence the speed of this process.

View Article: PubMed Central - PubMed

Affiliation: Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.

Show MeSH
Related in: MedlinePlus