Limits...
Subfunctionalization of sigma factors during the evolution of land plants based on mutant analysis of liverwort (Marchantia polymorpha L.) MpSIG1.

Ueda M, Takami T, Peng L, Ishizaki K, Kohchi T, Shikanai T, Nishimura Y - Genome Biol Evol (2013)

Bottom Line: The mutant did not show any visible phenotypes, implying that MpSIG1 function is redundant with that of other sigma factors.The transcript levels of genes clustered in the petL, psaA, psbB, psbK, and psbE operons of liverwort were lower than those in the wild type, a result similar to that in the SIG1 defective mutant in rice (Oryza sativa).Our study shows the ancestral function of SIG1 and the process of functional partitioning (subfunctionalization) of sigma factors during the evolution of land plants.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany, Graduate School of Science, Kyoto University, Japan.

ABSTRACT
Sigma factor is a subunit of plastid-encoded RNA polymerase that regulates the transcription of plastid-encoded genes by recognizing a set of promoters. Sigma factors have increased in copy number and have diversified during the evolution of land plants, but details of this process remain unknown. Liverworts represent the basal group of embryophytes and are expected to retain the ancestral features of land plants. In liverwort (Marchantia polymorpha L.), we isolated and characterized a T-DNA-tagged mutant (Mpsig1) of sigma factor 1 (MpSIG1). The mutant did not show any visible phenotypes, implying that MpSIG1 function is redundant with that of other sigma factors. However, quantitative reverse-transcription polymerase chain reaction and RNA gel blot analysis revealed that genes related to photosynthesis were downregulated, resulting in the minor reduction of some protein complexes. The transcript levels of genes clustered in the petL, psaA, psbB, psbK, and psbE operons of liverwort were lower than those in the wild type, a result similar to that in the SIG1 defective mutant in rice (Oryza sativa). Overexpression analysis revealed primitive functional divergence between the SIG1 and SIG2 proteins in bryophytes, whereas these proteins still retain functional redundancy. We also discovered that the predominant sigma factor for ndhF mRNA expression has been diversified in liverwort, Arabidopsis (Arabidopsis thaliana), and rice. Our study shows the ancestral function of SIG1 and the process of functional partitioning (subfunctionalization) of sigma factors during the evolution of land plants.

Show MeSH

Related in: MedlinePlus

CR-RT-PCR experiments on the psaA and ndhF genes in the liverwort and rice chloroplast genomes. CR-RT-PCR amplification of the chloroplast-encoded psaA and ndhF genes in liverwort (A) and rice (B). A schematic representation of the CR-RT-PCR results in liverwort (C) and rice (D). Arrows with angled lines and arrowheads with dotted lines show the transcription initiation sites and transcribed regions, respectively, for psaA and ndhF determined by CR-RT-PCR. The black triangles, which are not to scale, show the primer positions for CR-RT-PCR. The primer sequences are shown in supplementary table S2, Supplementary Material online. (E) An alignment of the psaA and ndhF regions upstream from the 5′-ends of the transcripts. The transcription initiation sites for angiosperm psaA and Arabidopsis were obtained from Tozawa et al. (2007) and Favory et al. (2005), respectively. Underlined letters indicate the −10 and −35 putative consensus motifs. (F) Comparison of nucleotide sequences in the promoter regions of ndhF in four representative Poaceae species. Ath, Arabidopsis thaliana; Hvu, Hordeum vulgare; Mpo, Marchantia polymorpha; Osa, Oryza sativa; Tae, Triticum aestivum; Zma, Zea mays.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3814195&req=5

evt137-F7: CR-RT-PCR experiments on the psaA and ndhF genes in the liverwort and rice chloroplast genomes. CR-RT-PCR amplification of the chloroplast-encoded psaA and ndhF genes in liverwort (A) and rice (B). A schematic representation of the CR-RT-PCR results in liverwort (C) and rice (D). Arrows with angled lines and arrowheads with dotted lines show the transcription initiation sites and transcribed regions, respectively, for psaA and ndhF determined by CR-RT-PCR. The black triangles, which are not to scale, show the primer positions for CR-RT-PCR. The primer sequences are shown in supplementary table S2, Supplementary Material online. (E) An alignment of the psaA and ndhF regions upstream from the 5′-ends of the transcripts. The transcription initiation sites for angiosperm psaA and Arabidopsis were obtained from Tozawa et al. (2007) and Favory et al. (2005), respectively. Underlined letters indicate the −10 and −35 putative consensus motifs. (F) Comparison of nucleotide sequences in the promoter regions of ndhF in four representative Poaceae species. Ath, Arabidopsis thaliana; Hvu, Hordeum vulgare; Mpo, Marchantia polymorpha; Osa, Oryza sativa; Tae, Triticum aestivum; Zma, Zea mays.

Mentions: First, a control experiment was performed to check the efficacy of first-strand cDNA preparation for CR-RT-PCR. The transcription initiation sites of psaA in liverwort and rice are surrounded by consensus PEP recognition motifs that are highly conserved among land plants. The 5′-end of the psaA CR-RT-PCR product was mapped to 148-nt and 129-nt upstream from the translation start codon of psaA in liverwort and rice, respectively (figs. 7C and D). The −35 and −10 consensus motifs are highly conserved in this region, suggesting that the promoter is conserved between liverwort and flowering plants and validating our CR-RT-PCR (fig. 7E).Fig. 7.—


Subfunctionalization of sigma factors during the evolution of land plants based on mutant analysis of liverwort (Marchantia polymorpha L.) MpSIG1.

Ueda M, Takami T, Peng L, Ishizaki K, Kohchi T, Shikanai T, Nishimura Y - Genome Biol Evol (2013)

CR-RT-PCR experiments on the psaA and ndhF genes in the liverwort and rice chloroplast genomes. CR-RT-PCR amplification of the chloroplast-encoded psaA and ndhF genes in liverwort (A) and rice (B). A schematic representation of the CR-RT-PCR results in liverwort (C) and rice (D). Arrows with angled lines and arrowheads with dotted lines show the transcription initiation sites and transcribed regions, respectively, for psaA and ndhF determined by CR-RT-PCR. The black triangles, which are not to scale, show the primer positions for CR-RT-PCR. The primer sequences are shown in supplementary table S2, Supplementary Material online. (E) An alignment of the psaA and ndhF regions upstream from the 5′-ends of the transcripts. The transcription initiation sites for angiosperm psaA and Arabidopsis were obtained from Tozawa et al. (2007) and Favory et al. (2005), respectively. Underlined letters indicate the −10 and −35 putative consensus motifs. (F) Comparison of nucleotide sequences in the promoter regions of ndhF in four representative Poaceae species. Ath, Arabidopsis thaliana; Hvu, Hordeum vulgare; Mpo, Marchantia polymorpha; Osa, Oryza sativa; Tae, Triticum aestivum; Zma, Zea mays.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814195&req=5

evt137-F7: CR-RT-PCR experiments on the psaA and ndhF genes in the liverwort and rice chloroplast genomes. CR-RT-PCR amplification of the chloroplast-encoded psaA and ndhF genes in liverwort (A) and rice (B). A schematic representation of the CR-RT-PCR results in liverwort (C) and rice (D). Arrows with angled lines and arrowheads with dotted lines show the transcription initiation sites and transcribed regions, respectively, for psaA and ndhF determined by CR-RT-PCR. The black triangles, which are not to scale, show the primer positions for CR-RT-PCR. The primer sequences are shown in supplementary table S2, Supplementary Material online. (E) An alignment of the psaA and ndhF regions upstream from the 5′-ends of the transcripts. The transcription initiation sites for angiosperm psaA and Arabidopsis were obtained from Tozawa et al. (2007) and Favory et al. (2005), respectively. Underlined letters indicate the −10 and −35 putative consensus motifs. (F) Comparison of nucleotide sequences in the promoter regions of ndhF in four representative Poaceae species. Ath, Arabidopsis thaliana; Hvu, Hordeum vulgare; Mpo, Marchantia polymorpha; Osa, Oryza sativa; Tae, Triticum aestivum; Zma, Zea mays.
Mentions: First, a control experiment was performed to check the efficacy of first-strand cDNA preparation for CR-RT-PCR. The transcription initiation sites of psaA in liverwort and rice are surrounded by consensus PEP recognition motifs that are highly conserved among land plants. The 5′-end of the psaA CR-RT-PCR product was mapped to 148-nt and 129-nt upstream from the translation start codon of psaA in liverwort and rice, respectively (figs. 7C and D). The −35 and −10 consensus motifs are highly conserved in this region, suggesting that the promoter is conserved between liverwort and flowering plants and validating our CR-RT-PCR (fig. 7E).Fig. 7.—

Bottom Line: The mutant did not show any visible phenotypes, implying that MpSIG1 function is redundant with that of other sigma factors.The transcript levels of genes clustered in the petL, psaA, psbB, psbK, and psbE operons of liverwort were lower than those in the wild type, a result similar to that in the SIG1 defective mutant in rice (Oryza sativa).Our study shows the ancestral function of SIG1 and the process of functional partitioning (subfunctionalization) of sigma factors during the evolution of land plants.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany, Graduate School of Science, Kyoto University, Japan.

ABSTRACT
Sigma factor is a subunit of plastid-encoded RNA polymerase that regulates the transcription of plastid-encoded genes by recognizing a set of promoters. Sigma factors have increased in copy number and have diversified during the evolution of land plants, but details of this process remain unknown. Liverworts represent the basal group of embryophytes and are expected to retain the ancestral features of land plants. In liverwort (Marchantia polymorpha L.), we isolated and characterized a T-DNA-tagged mutant (Mpsig1) of sigma factor 1 (MpSIG1). The mutant did not show any visible phenotypes, implying that MpSIG1 function is redundant with that of other sigma factors. However, quantitative reverse-transcription polymerase chain reaction and RNA gel blot analysis revealed that genes related to photosynthesis were downregulated, resulting in the minor reduction of some protein complexes. The transcript levels of genes clustered in the petL, psaA, psbB, psbK, and psbE operons of liverwort were lower than those in the wild type, a result similar to that in the SIG1 defective mutant in rice (Oryza sativa). Overexpression analysis revealed primitive functional divergence between the SIG1 and SIG2 proteins in bryophytes, whereas these proteins still retain functional redundancy. We also discovered that the predominant sigma factor for ndhF mRNA expression has been diversified in liverwort, Arabidopsis (Arabidopsis thaliana), and rice. Our study shows the ancestral function of SIG1 and the process of functional partitioning (subfunctionalization) of sigma factors during the evolution of land plants.

Show MeSH
Related in: MedlinePlus