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Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement.

Blazier JC, Ruhlman TA, Weng ML, Rehman SK, Sabir JS, Jansen RK - Sci Rep (2016)

Bottom Line: Multiple lines of evidence indicated that the rpoA sequences are likely functional despite retaining as low as 30% nucleotide sequence identity with rpoA genes from outgroups in the same angiosperm order.The plastid genomes containing these divergent rpoA genes have experienced extensive structural rearrangement, including large expansions of the inverted repeat.We propose that illegitimate recombination, not positive selection, has driven the divergence of rpoA.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.

ABSTRACT
Genes for the plastid-encoded RNA polymerase (PEP) persist in the plastid genomes of all photosynthetic angiosperms. However, three unrelated lineages (Annonaceae, Passifloraceae and Geraniaceae) have been identified with unusually divergent open reading frames (ORFs) in the conserved region of rpoA, the gene encoding the PEP α subunit. We used sequence-based approaches to evaluate whether these genes retain function. Both gene sequences and complete plastid genome sequences were assembled and analyzed from each of the three angiosperm families. Multiple lines of evidence indicated that the rpoA sequences are likely functional despite retaining as low as 30% nucleotide sequence identity with rpoA genes from outgroups in the same angiosperm order. The ratio of non-synonymous to synonymous substitutions indicated that these genes are under purifying selection, and bioinformatic prediction of conserved domains indicated that functional domains are preserved. One of the lineages (Pelargonium, Geraniaceae) contains species with multiple rpoA-like ORFs that show evidence of ongoing inter-paralog gene conversion. The plastid genomes containing these divergent rpoA genes have experienced extensive structural rearrangement, including large expansions of the inverted repeat. We propose that illegitimate recombination, not positive selection, has driven the divergence of rpoA.

No MeSH data available.


Related in: MedlinePlus

Alignment of PEP promoter regions.(A) Alignment of promoter region for rbcL in three species with functional PEP (Nicotiana tabacum, Arabidopsis thaliana, Pelargonium x hortorum) and one lacking PEP (Cuscuta obtusiflora). (B) Alignment of promoter region for psbA in three species with functional PEP (N. tabacum, A. thaliana, P. x hortorum) and one lacking PEP (C. obtusiflora). The conserved −10 and −35 elements are indicated by block arrows and the transcription start site is indicated by a red box (+1).
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f1: Alignment of PEP promoter regions.(A) Alignment of promoter region for rbcL in three species with functional PEP (Nicotiana tabacum, Arabidopsis thaliana, Pelargonium x hortorum) and one lacking PEP (Cuscuta obtusiflora). (B) Alignment of promoter region for psbA in three species with functional PEP (N. tabacum, A. thaliana, P. x hortorum) and one lacking PEP (C. obtusiflora). The conserved −10 and −35 elements are indicated by block arrows and the transcription start site is indicated by a red box (+1).

Mentions: In silico examination of PEP promoters upstream of the rbcL and psbA coding regions revealed that P. x hortorum sequences closely resembled those of A. thaliana and N. tabacum. The -35 and -10 elements, as well as the transcription start sites, were 100% identical across all three species, unlike in Cuscuta obtusiflora, a parasitic plant lacking PEP (Fig. 1A,B).


Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement.

Blazier JC, Ruhlman TA, Weng ML, Rehman SK, Sabir JS, Jansen RK - Sci Rep (2016)

Alignment of PEP promoter regions.(A) Alignment of promoter region for rbcL in three species with functional PEP (Nicotiana tabacum, Arabidopsis thaliana, Pelargonium x hortorum) and one lacking PEP (Cuscuta obtusiflora). (B) Alignment of promoter region for psbA in three species with functional PEP (N. tabacum, A. thaliana, P. x hortorum) and one lacking PEP (C. obtusiflora). The conserved −10 and −35 elements are indicated by block arrows and the transcription start site is indicated by a red box (+1).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4834550&req=5

f1: Alignment of PEP promoter regions.(A) Alignment of promoter region for rbcL in three species with functional PEP (Nicotiana tabacum, Arabidopsis thaliana, Pelargonium x hortorum) and one lacking PEP (Cuscuta obtusiflora). (B) Alignment of promoter region for psbA in three species with functional PEP (N. tabacum, A. thaliana, P. x hortorum) and one lacking PEP (C. obtusiflora). The conserved −10 and −35 elements are indicated by block arrows and the transcription start site is indicated by a red box (+1).
Mentions: In silico examination of PEP promoters upstream of the rbcL and psbA coding regions revealed that P. x hortorum sequences closely resembled those of A. thaliana and N. tabacum. The -35 and -10 elements, as well as the transcription start sites, were 100% identical across all three species, unlike in Cuscuta obtusiflora, a parasitic plant lacking PEP (Fig. 1A,B).

Bottom Line: Multiple lines of evidence indicated that the rpoA sequences are likely functional despite retaining as low as 30% nucleotide sequence identity with rpoA genes from outgroups in the same angiosperm order.The plastid genomes containing these divergent rpoA genes have experienced extensive structural rearrangement, including large expansions of the inverted repeat.We propose that illegitimate recombination, not positive selection, has driven the divergence of rpoA.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.

ABSTRACT
Genes for the plastid-encoded RNA polymerase (PEP) persist in the plastid genomes of all photosynthetic angiosperms. However, three unrelated lineages (Annonaceae, Passifloraceae and Geraniaceae) have been identified with unusually divergent open reading frames (ORFs) in the conserved region of rpoA, the gene encoding the PEP α subunit. We used sequence-based approaches to evaluate whether these genes retain function. Both gene sequences and complete plastid genome sequences were assembled and analyzed from each of the three angiosperm families. Multiple lines of evidence indicated that the rpoA sequences are likely functional despite retaining as low as 30% nucleotide sequence identity with rpoA genes from outgroups in the same angiosperm order. The ratio of non-synonymous to synonymous substitutions indicated that these genes are under purifying selection, and bioinformatic prediction of conserved domains indicated that functional domains are preserved. One of the lineages (Pelargonium, Geraniaceae) contains species with multiple rpoA-like ORFs that show evidence of ongoing inter-paralog gene conversion. The plastid genomes containing these divergent rpoA genes have experienced extensive structural rearrangement, including large expansions of the inverted repeat. We propose that illegitimate recombination, not positive selection, has driven the divergence of rpoA.

No MeSH data available.


Related in: MedlinePlus