Edited by: Jun Yu, Beijing Institute of Genomics, China
Reviewed by: Stewart Gillmor, CINVESTAV-IPN, Mexico; Swarup Kumar Parida, National Institute of Plant Genome Research, India
*Correspondence: María Eugenia Zanetti, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, CCT-CONICET, Calle 115 y 47, C. P. 1900, La Plata, Argentina e-mail:
This article was submitted to Plant Genetics and Genomics, a section of the journal Frontiers in Plant Science.
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In the past decade, plant nuclear factor Y (NF-Y) genes have gained major interest due to their roles in many biological processes in plant development or adaptation to environmental conditions, particularly in the root nodule symbiosis established between legume plants and nitrogen fixing bacteria. NF-Ys are heterotrimeric transcriptional complexes composed of three subunits, NF-YA, NF-YB, and NF-YC, which bind with high affinity and specificity to the CCAAT box, a
Nuclear factor Ys (NF-Ys) are heterotrimeric transcription factors evolutionary conserved in yeast, mammals and plants that have emerged as important regulators of gene expression. The complex is composed of three subunits: NF-YA, NF-YB, and NF-YC (also known as HAP2, HAP3, and HAP5, respectively). The current model for assembling of the NF-Y complex in mammals involves the dimerization of the NF-YB and NF-YC subunits through the interaction of their histone-fold domains (HFDs) in the cytoplasm, the translocation of the heterodimer to the nucleus and the association with the NF-YA subunit to form the mature and functional complex (Kahle et al.,
In yeast and metazoan, each NF-Y subunit is encoded by one or two genes, whereas plant families have largely expanded (Petroni et al.,
The expansion of the NF-Y gene family in the plant lineage could result theoretically in more than a thousand alternative unique heterotrimeric combinations (Siefers et al.,
The function of the NF-Y complex has been extensively characterized in mammals, where it plays a central role in the control of cell proliferation and early stages of development. In plants, forward and reverse genetic approaches have led to the identification of several genes encoding NF-Y subunits that are required for the correct development of plant programs such as embryogenesis (Lotan et al.,
Expression analyses of individual members of each NF-Y family conducted in
Common bean is the most important grain legume for human consumption, representing the major source of proteins and essential nutrients in the diets of developing countries. This species is original of America, where two main centers of genetic diversification have been proposed: the Mesoamerican and the South Andean centers (Gepts,
Considering the important role played by NF-Y genes in root nodule symbiosis, we took advantage of the recently released genome of common bean v1.0 (Schmutz et al.,
Individual subunits were identified by TBLASTN searches against the common bean genome V1.0 database (
Seeds of common bean (NAG12 accession) were surface sterilized and germinated on wet paper for 2–3 days at 26°C in the dark as previously described (Peltzer Meschini et al.,
Total RNA extraction was performed with Trizol following manufacture's instructions (Invitrogen). RNA concentration was determined by measuring absorbance at 260 nm in a Nanodrop ND-1000 (Nanodrop Technologies Inc.,
We used the full length amino acid sequences of the 30 members of Arabidopsis NF-Y gene family to sequentially BLAST search the
PvNF-YA1 | Phvul.001G196800 | NF-YA10 (AT5G06510) | PvNF-YB1 | Phvul.008G278900 | NF-YB3 (AT4G14540) | PvNF-YC1 | Phvul.006G093200 | NF-YC9 (AT1G08970) |
PvNF-YA2 | Phvul.002G246600 | NF-YA7 (AT1G30500) | PvNF-YB2 | Phvul.007G134000 | NF-YB8 (AT2G37060) | PvNF-YC2 | Phvul.005G050000 | NF-YC2 (AT1G56170) |
PvNF-YA3 | Phvul.005G156100 | NF-YA8 (AT1G17590) | PvNF-YB3 | Phvul.006G139400 | NF-YB3 (AT4G14540) | PvNF-YC3 | Phvul.010G102300 | NF-YC4 (AT5G63470) |
PvNF-YA4 | Phvul.003G133100 | NF-YA3 (AT1G72830) | PvNF-YB4 | Phvul.002G264300 | NF-YB3 (AT4G14540) | PvNF-YC4 | Phvul.009G166000 | NF-YC1 (AT3G48590) |
PvNF-YA5 | Phvul.008G283100 | NF-YA9 (AT3G20910) | PvNF-YB5 | Phvul.007G163100 | NF-YB10 (AT3G53340) | PvNF-YC5 | Phvul.006G152400 | NF-YC2 (AT1G56170) |
PvNF-YA6 | Phvul.011G211300 | NF-YA9 (AT3G20910) | PvNF-YB6 | Phvul.007G165100 | NF-YB5 (AT2G47810 | PvNF-YC6 | Phvul.007G181400 | NF-YC9 (AT1G08970) |
PvNF-YA7 | Phvul.006G062200 | NF-YA1 (AT5G12840) | PvNF-YB7 | Phvul.003G086800 | NF-YB3 (AT4G14540) | PvNF-YC7 | Phvul.010G082500 | NF-YC3 (AT1G54830) |
PvNF-YA8 | Phvul.010G133300 | NF-YA3 (AT1G72830) | PvNF-YB8 | Phvul.002G273800 | NF-YB7 (AT2G13570) | |||
PvNF-YA9 | Phvul.007G267100 | NF-YA10 (AT5G06510) | PvNF-YB9 | Phvul.009G155500 | NF-YB7 (AT2G13570) | |||
PvNF-YB10 | Phvul.009G246400 | NF-YB5 (AT2G47810) | ||||||
PvNF-YB11 | Phvul.003G103500 | NF-YB5 (AT2G47810) | ||||||
PvNF-YB12 | Phvul.007G234800 | NF-YB6 (AT5G47670) | ||||||
PvNF-YB13 | Phvul.007G195900 | NF-YB4 (AT1G09030) | ||||||
PvNF-YB14 | Phvul.001G174600 | NFY-B10 (AT3G53340) |
The gene structure analysis revealed that members of the NF-YA family have a complex intron/exon organization with 5–7 introns per gene, distributed mainly along the 5′ UTRs and the coding regions, being
In contrast to the
Multiple alignments for each PvNF-Y subunit families were constructed using ClustalW (Thompson et al.,
PvNF-YA proteins are variable in length, ranging between 234 and 349 amino acids. The conserved central region is composed of 53 amino acids and contains two characteristic domains with separated functions (Figure
The PvNF-YB family is composed of 14 members of variable length (132–229 amino acids), which are highly similar in the 96 amino acids that define the conserved central domain involved in the interaction with NF-YC and NF-YA subunits and DNA binding (Figure
The PvNF-YC family contains a central domain of 80 amino acids that is highly conserved across the different members, but also with the NF-YC mouse counterpart (Figure
Individual members of the NF-Y subunits have shown a tissue specific expression pattern in other plant species (Stephenson et al.,
Analysis of the PvNF-YA family revealed that all members have detectable transcript levels in at least one of the organs examined (Figure
Analysis of the
The expression analysis of PvNF-YC members in different organs (Figure
In the past decade, plant NF-Y genes have gained major interest due to their roles in plant development or in the response to changing environmental conditions, particularly in the root nodule symbiosis. In this work, we have annotated and characterized 9, 14 and 7 members of
The gene-structure analysis of the
In the context of the root nodule symbiosis, we identified two members of the
In the past 10 years, an increasing amount of genetic and biochemical evidences have supported the importance of the NF-Y family of proteins in different developmental processes along the lifespan of plants, as well as in their adaptation to adverse environmental conditions. Here, we have generated an initial dataset of sequences, intron/exon arrangements and expression patterns of genes encoding NF-Y subunits in
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
We thank Ulises Villagra, Claudio Mazo, Paula Giménez and Silvana Tongiani for technical assistance. We also thank Andreas Niebel and Maël Baudin for fruitful discussions. This work was financially supported by grants from ANPCyT, Argentina (PICT 2008-0443, PICT 2010-2431, and PICT 2010-2722) and from a CONICET-CNRS cooperative program.
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