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Identification, classification and transcriptional profiles of dirigent domain-containing proteins in sugarcane

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Abstract

Dirigent (DIR) proteins, encoded by DIR genes, are referred to as “dirigent” because they direct the outcome of the coupling of the monolignol coniferyl alcohol into (+) or (−) pinoresinol, the first intermediates in the enantiocomplementary pathways for lignan biosynthesis. DIR domain-containing or DIR-like proteins are, thus, termed for not having a clear characterization. A transcriptome- and genome-wide survey of DIR domain-containing proteins in sugarcane was carried out, in addition to phylogenetic, physicochemical and transcriptional analyses. A total of 120 non-redundant sequences containing the DIR domain were identified and classified into 64 groups according to phylogenetic and sequence alignment analyses. In silico analysis of transcript abundance showed that these sequences are expressed at low levels in leaves and genes in the same phylogenetic clade have similar expression patterns. Expression analysis of ShDIR1-like transcripts in the culm internodes of sugarcane demonstrates their abundance in mature internodes, their induction by nitrogen fertilization and their predominant expression in cells that have a lignified secondary cell wall, such as vascular bundles of young internodes and parenchymal cells of the pith of mature internodes. Due to the lack of information about the functional role of DIR in plants, a possible relationship is discussed between the ShDIR1-like transcriptional profile and cell wall development in parenchyma cells of sugarcane culm, which typically accumulates large amounts of sucrose. The number of genes encoding the DIR domain-containing proteins in sugarcane is intriguing and is an indication per se that these proteins may have an important metabolic role and thus deserve to be better studied.

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Acknowledgements

We acknowledge Fundação de Amparo a Pesquisa do Estado de São Paulo (FAPESP) for financial support (2008/58035-6) and fellowships granted to PMN (2010/08232-0 and 2012/08540-1) and MSB (2010/11476-8). We thank Laerti Reis Roque for technical support, Pedro Araújo for advice in the in situ hybridization experiments and Larissa M. Andrade for figure preparation. AB and PM thank the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, Coordination for the Improvement of Higher Education Personnel) and the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, National Council for Scientific and Technological Development) for Ph.D. and Research fellowships, respectively.

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Authors and Affiliations

  1. Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, Campinas, SP, 13083-970, Brazil

    Paula Macedo Nobile, Alexandra Bottcher, Juliana L. S. Mayer, Michael S. Brito & Paulo Mazzafera

  2. Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana, Instituto Agronômico de Campinas, CP 206, Ribeirão Preto, SP, 14001-970, Brazil

    Paula Macedo Nobile, Michael S. Brito, Ivan A. dos Anjos, Marcos Guimarães de Andrade Landell & Silvana Creste

  3. Centro de Biologia Molecular e Engenharia Genética, CEBMEG, Universidade Estadual de Campinas, Campinas, SP, 13083-875, Brazil

    Renato Vicentini

  4. Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, Campinas, SP, CEP 13083-970, Brazil

    Diego Mauricio Riaño-Pachón

Authors
  1. Paula Macedo Nobile
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  2. Alexandra Bottcher
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  3. Juliana L. S. Mayer
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  4. Michael S. Brito
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  5. Ivan A. dos Anjos
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  6. Marcos Guimarães de Andrade Landell
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  7. Renato Vicentini
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  8. Silvana Creste
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  9. Diego Mauricio Riaño-Pachón
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  10. Paulo Mazzafera
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Corresponding authors

Correspondence to Paula Macedo Nobile, Diego Mauricio Riaño-Pachón or Paulo Mazzafera.

Additional information

Communicated by S. Hohmann.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Data S1. The sugarcane DIR domain-containing protein amino acid sequences in Fasta format (FASTA 86 kb)

438_2017_1349_MOESM2_ESM.fasta.clstr

Data S2. The sugarcane DIR domain-containing protein sequences obtained from different databases clustered with at least 96% of identity (FASTA.CLSTR 16 kb)

Data S3. Percent Identity Matrix of Dir-c amino acid sequences generated by Clustal2.1 (XLSX 91 kb)

Supplementary material 4 (PDF 2772 kb)

Supplementary material 5 (PDF 674 kb)

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Nobile, P.M., Bottcher, A., Mayer, J.L.S. et al. Identification, classification and transcriptional profiles of dirigent domain-containing proteins in sugarcane. Mol Genet Genomics 292, 1323–1340 (2017). https://doi.org/10.1007/s00438-017-1349-6

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  • DOI: https://doi.org/10.1007/s00438-017-1349-6

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