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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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RNA gel blot hybridizations for chloroplast-encoded genes in the Mpsig1 mutant. Specific probes for each gene were prepared using primer pairs listed in supplementary table S3, Supplementary Material online. Fifteen-day-old plants grown under continuous white light (40 μmol photons m−2 s−1) at 20 °C were used. Equal loading was confirmed by comparing the ethidium bromide staining of rRNA.
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evt137-F3: RNA gel blot hybridizations for chloroplast-encoded genes in the Mpsig1 mutant. Specific probes for each gene were prepared using primer pairs listed in supplementary table S3, Supplementary Material online. Fifteen-day-old plants grown under continuous white light (40 μmol photons m−2 s−1) at 20 °C were used. Equal loading was confirmed by comparing the ethidium bromide staining of rRNA.

Mentions: To assess whether the Mpsig1 mutant phenotype observed in chloroplast RNA was due to the lack of MpSIG1, the mutant was transformed with a WT copy of MpSIG1 cDNA controlled by the CaMV 35S promoter and the NOS transcription terminator. Compared with the WT plants, the complemented lines accumulated approximately a 19-fold higher level of the MpSIG1 transcript (fig. 2C). The overexpression of MpSIG1 did not cause any visible abnormality (fig. 1B). The transcript levels of the genes that were downregulated in the Mpsig1 mutant became even higher in the complemented lines than in the WT plants (fig. 2A and B). In particular, ndhF, rps18, and psbK transcript levels were more than twice as high as those in the WT plants, probably because of the overexpression of MpSIG1 (fig. 2B). Furthermore, more than 1.5-fold up-regulation in overexpressors was observed for nine transcripts (atpB, chlB, ndhC, ndhH, petA, psaC, rpoC1, rps7, and ycf1) that were not significantly affected in the Mpsig1 mutant (fig. 2D). The validity of the qRT-PCR was confirmed by performing Northern hybridization analysis for six selected transcripts (ndhF, psaA, psbB, psbD, psbE/psbF, and rpl33/rps18) (fig. 3). On the basis of the phenotypes of the mutant and overexpressors (complemented lines), it is highly likely that MpSIG1 is involved in the transcription of a wide range of transcripts and that its function overlaps with and/or is complemented by those of other sigma factors. We could not eliminate the possibility that some of the mutant phenotypes observed in the RNA expression levels are due to a secondary effect from disturbance of the sigma factor network.Fig. 3.—


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)

RNA gel blot hybridizations for chloroplast-encoded genes in the Mpsig1 mutant. Specific probes for each gene were prepared using primer pairs listed in supplementary table S3, Supplementary Material online. Fifteen-day-old plants grown under continuous white light (40 μmol photons m−2 s−1) at 20 °C were used. Equal loading was confirmed by comparing the ethidium bromide staining of rRNA.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evt137-F3: RNA gel blot hybridizations for chloroplast-encoded genes in the Mpsig1 mutant. Specific probes for each gene were prepared using primer pairs listed in supplementary table S3, Supplementary Material online. Fifteen-day-old plants grown under continuous white light (40 μmol photons m−2 s−1) at 20 °C were used. Equal loading was confirmed by comparing the ethidium bromide staining of rRNA.
Mentions: To assess whether the Mpsig1 mutant phenotype observed in chloroplast RNA was due to the lack of MpSIG1, the mutant was transformed with a WT copy of MpSIG1 cDNA controlled by the CaMV 35S promoter and the NOS transcription terminator. Compared with the WT plants, the complemented lines accumulated approximately a 19-fold higher level of the MpSIG1 transcript (fig. 2C). The overexpression of MpSIG1 did not cause any visible abnormality (fig. 1B). The transcript levels of the genes that were downregulated in the Mpsig1 mutant became even higher in the complemented lines than in the WT plants (fig. 2A and B). In particular, ndhF, rps18, and psbK transcript levels were more than twice as high as those in the WT plants, probably because of the overexpression of MpSIG1 (fig. 2B). Furthermore, more than 1.5-fold up-regulation in overexpressors was observed for nine transcripts (atpB, chlB, ndhC, ndhH, petA, psaC, rpoC1, rps7, and ycf1) that were not significantly affected in the Mpsig1 mutant (fig. 2D). The validity of the qRT-PCR was confirmed by performing Northern hybridization analysis for six selected transcripts (ndhF, psaA, psbB, psbD, psbE/psbF, and rpl33/rps18) (fig. 3). On the basis of the phenotypes of the mutant and overexpressors (complemented lines), it is highly likely that MpSIG1 is involved in the transcription of a wide range of transcripts and that its function overlaps with and/or is complemented by those of other sigma factors. We could not eliminate the possibility that some of the mutant phenotypes observed in the RNA expression levels are due to a secondary effect from disturbance of the sigma factor network.Fig. 3.—

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