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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.

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The levels of plastid transcripts in the Mpsig1 mutant and its complemented lines. The abundance of mRNAs, tRNAs, and rRNA transcripts was measured in the Mpsig1 mutant using qRT-PCR. (A, B, D, and E) Expression levels of chloroplast-encoded genes. (A) Genes that are downregulated in the Mpsig1 mutant. (B) Genes downregulated by more than 30% in the Mpsig1 mutant. (C) Expression levels of MpSIG1 in the nucleus. (D) Genes upregulated by at least 1.5-fold in the complemented Mpsig1 mutant. (E) Other genes. The standard deviations (n = 3, n stands for technical replicates) are indicated by lines extending from the bars. Each mean represents the ratio of the expression level of transcripts in the Mpsig1 mutant or complemented plants compared with that of WT plants. The means are depicted by white and gray bars for the Mpsig1 mutant (Mpsig1) and complemented plant (Mpsig1 + P35S:MpSIG1), respectively. Fifteen-day-old plants grown under continuous white light (40 μmol photons m−2 s−1) at 20 °C were used.
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evt137-F2: The levels of plastid transcripts in the Mpsig1 mutant and its complemented lines. The abundance of mRNAs, tRNAs, and rRNA transcripts was measured in the Mpsig1 mutant using qRT-PCR. (A, B, D, and E) Expression levels of chloroplast-encoded genes. (A) Genes that are downregulated in the Mpsig1 mutant. (B) Genes downregulated by more than 30% in the Mpsig1 mutant. (C) Expression levels of MpSIG1 in the nucleus. (D) Genes upregulated by at least 1.5-fold in the complemented Mpsig1 mutant. (E) Other genes. The standard deviations (n = 3, n stands for technical replicates) are indicated by lines extending from the bars. Each mean represents the ratio of the expression level of transcripts in the Mpsig1 mutant or complemented plants compared with that of WT plants. The means are depicted by white and gray bars for the Mpsig1 mutant (Mpsig1) and complemented plant (Mpsig1 + P35S:MpSIG1), respectively. Fifteen-day-old plants grown under continuous white light (40 μmol photons m−2 s−1) at 20 °C were used.

Mentions: Despite the complete loss of the functional MpSIG1 gene, the mutant did not show any visible phenotypes (fig. 1B); however, transcription in chloroplasts might be affected to some extent. To assess this possibility, we measured the relative transcript abundance of 33 plastid-encoded genes expressed in the WT plant, the Mpsig1 mutant and the Mpsig1 mutant complemented by introduction of MpSIG1 cDNA. Supplementary figure S1, Supplementary Material online, summarizes the genes used for the mRNA expression analysis. In rice, OsSIG1 is involved in the transcription of at least three operons, psaA/psaB/rps14, psbB/psbT/psbH/petB/petD, and psbE/psbF/psbL/psbJ (Tozawa et al. 2007). In the Mpsig1 mutant, the levels of petB, psaA, psaB, psbB, psbE, psbF, and rps14 were mildly reduced (fig. 2A). The accumulation levels of these transcripts were approximately 60–90% of the WT plants (supplementary table S6, Supplementary Material online), suggesting that the function of MpSIG1 overlaps with that of other sigma factors in the WT plant and/or that its function is partially complemented by other sigma factors in the mutant. In addition, more than a 30% reduction was observed for three other genes (ndhF, psbK, and rps18) (fig. 2B). The transcript abundances of ndhF, rps18 (petL operon: petL/petG/psaJ/rpl33/rps18), and psbK (psbK operon: psbK/psbI) were also reduced to 48%, 65%, and 67% compared with those of WT plants, respectively (supplementary table S6, Supplementary Material online).Fig. 2.—


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)

The levels of plastid transcripts in the Mpsig1 mutant and its complemented lines. The abundance of mRNAs, tRNAs, and rRNA transcripts was measured in the Mpsig1 mutant using qRT-PCR. (A, B, D, and E) Expression levels of chloroplast-encoded genes. (A) Genes that are downregulated in the Mpsig1 mutant. (B) Genes downregulated by more than 30% in the Mpsig1 mutant. (C) Expression levels of MpSIG1 in the nucleus. (D) Genes upregulated by at least 1.5-fold in the complemented Mpsig1 mutant. (E) Other genes. The standard deviations (n = 3, n stands for technical replicates) are indicated by lines extending from the bars. Each mean represents the ratio of the expression level of transcripts in the Mpsig1 mutant or complemented plants compared with that of WT plants. The means are depicted by white and gray bars for the Mpsig1 mutant (Mpsig1) and complemented plant (Mpsig1 + P35S:MpSIG1), respectively. Fifteen-day-old plants grown under continuous white light (40 μmol photons m−2 s−1) at 20 °C were used.
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Related In: Results  -  Collection

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evt137-F2: The levels of plastid transcripts in the Mpsig1 mutant and its complemented lines. The abundance of mRNAs, tRNAs, and rRNA transcripts was measured in the Mpsig1 mutant using qRT-PCR. (A, B, D, and E) Expression levels of chloroplast-encoded genes. (A) Genes that are downregulated in the Mpsig1 mutant. (B) Genes downregulated by more than 30% in the Mpsig1 mutant. (C) Expression levels of MpSIG1 in the nucleus. (D) Genes upregulated by at least 1.5-fold in the complemented Mpsig1 mutant. (E) Other genes. The standard deviations (n = 3, n stands for technical replicates) are indicated by lines extending from the bars. Each mean represents the ratio of the expression level of transcripts in the Mpsig1 mutant or complemented plants compared with that of WT plants. The means are depicted by white and gray bars for the Mpsig1 mutant (Mpsig1) and complemented plant (Mpsig1 + P35S:MpSIG1), respectively. Fifteen-day-old plants grown under continuous white light (40 μmol photons m−2 s−1) at 20 °C were used.
Mentions: Despite the complete loss of the functional MpSIG1 gene, the mutant did not show any visible phenotypes (fig. 1B); however, transcription in chloroplasts might be affected to some extent. To assess this possibility, we measured the relative transcript abundance of 33 plastid-encoded genes expressed in the WT plant, the Mpsig1 mutant and the Mpsig1 mutant complemented by introduction of MpSIG1 cDNA. Supplementary figure S1, Supplementary Material online, summarizes the genes used for the mRNA expression analysis. In rice, OsSIG1 is involved in the transcription of at least three operons, psaA/psaB/rps14, psbB/psbT/psbH/petB/petD, and psbE/psbF/psbL/psbJ (Tozawa et al. 2007). In the Mpsig1 mutant, the levels of petB, psaA, psaB, psbB, psbE, psbF, and rps14 were mildly reduced (fig. 2A). The accumulation levels of these transcripts were approximately 60–90% of the WT plants (supplementary table S6, Supplementary Material online), suggesting that the function of MpSIG1 overlaps with that of other sigma factors in the WT plant and/or that its function is partially complemented by other sigma factors in the mutant. In addition, more than a 30% reduction was observed for three other genes (ndhF, psbK, and rps18) (fig. 2B). The transcript abundances of ndhF, rps18 (petL operon: petL/petG/psaJ/rpl33/rps18), and psbK (psbK operon: psbK/psbI) were also reduced to 48%, 65%, and 67% compared with those of WT plants, respectively (supplementary table S6, Supplementary Material online).Fig. 2.—

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