Elsevier

Gene

Volume 326, 4 February 2004, Pages 13-22
Gene

Ordered origin of the typical two- and three-repeat Myb genes

https://doi.org/10.1016/j.gene.2003.09.049Get rights and content

Abstract

Myb domain proteins contain a conserved DNA-binding domain composed of one to four conserved repeat motifs. In animals, Myb proteins are encoded by a small gene family and commonly contain three repeat motifs (R1R2R3); whereas, plant Myb proteins are encoded by a very large and diverse gene family in which a motif containing two repeats (R2R3) is the most common. In contrast to the conservation in the Myb domain, other regions of Myb proteins are highly variable. To explore the evolutionary origin of Myb genes, we cloned and sequenced Myb domains from maize and sorghum, and conducted a comprehensive phylogenetic analysis of Myb genes. The results indicate that the origins of individual Myb repeats are strikingly distinct, and that the R2 repeat has evolved more slowly than the R1 and R3 repeats. However, it is not clear which repeat is the most ancient one. The evidence also suggests that R2R3 and R1R2R3 Myb genes co-existed in eukaryotes before the divergence of plants and animals. Based on our results, we propose that R1R2R3 Myb genes were derived from R2R3 Myb genes by gain of the R1 repeat through an ancient intragenic duplication; this gain model is more parsimonious than the previous proposal that R2R3 Myb genes were derived from R1R2R3 Mybs by loss of the R1 repeat. A separate group of diverse non-typical Myb proteins exhibits a polyphyletic origin and a complex evolutionary pattern. Finally, a small group of ancient Myb paralogs prior to the amplification of current Myb genes is identified. Together, these results support a new model for the ordered evolution of Myb gene family.

Introduction

The Myb gene super-family comprises a group of related genes found in plant, animal, and fungal genomes. The archetype is the v-myb oncogene from Avian Myeloblastosis Virus (Klempnauer et al., 1982). Subsequently, members of the Myb gene family were identified in diverse plants and animals (Rosinski and Atchley, 1998). Myb genes encode proteins with DNA-binding domains composed of one, two or three semi-conserved motifs of approximately 50 amino acids each. Each motif is capable of forming 3 α-helices; the 3rd α-helix is thought to play a recognition role in binding to a short DNA sequence (Rabinowicz et al., 1999). Many Myb proteins contain two or three tandem repeats of the motif (referred to as R1, R2, and R3 repeat, respectively) within a single protein (Lipsick, 1996). A 4-repeat Myb gene was reported in Arabidopsis (Stracke et al., 2001).

Vertebrate genomes are reported to contain relatively few Myb genes (Rosinski and Atchley, 1998); these are classified on a functional basis into three general forms, A-Myb, B-Myb and C-Myb (Lipsick, 1996). In contrast to animals, flowering plants contain large numbers of Myb genes. For example, 125 R2R3 Myb genes have been identified in Arabidopsis (Stracke et al., 2001). Surveys based on expressed sequences have detected more than 80 Myb genes in maize (Rabinowicz et al., 1999), approximately 30 in Petunia hybrida (Avila et al., 1993), and approximately 200 Myb genes in cotton (Cedroni et al., 2003). Moreover, plant Myb genes are structurally and functionally very diverse. The functions of most plant Myb genes are unknown, although analysis of some well-studied examples indicates three well-defined roles for plant Myb transcription factors to date: (1) controlling secondary metabolism, particularly in flavonoid biosynthesis (Grotewold et al., 1994); (2) regulating cellular morphogenesis (Oppenheimer et al., 1991); (3) mediating signal transduction pathways, such as in response to abiotic stress (Urao et al., 1993) and pathogen attack (Yang and Klessig, 1996). In addition, some plant Myb proteins may serve structural roles as in the case of RTBP1, a Myb-domain protein implicated in plant telomere function (Yu et al., 2000).

It should be noted that a group of Myb proteins containing only one or a partial Myb repeat was found in Drosophila (England et al., 1992) and in plants (Baranowskij et al., 1994). Additionally, some Myb proteins with two or three repeats in fungi and plants lack the typical constantly spaced Trp residues. These proteins with atypical Trp spacing or partial Myb domains are non-typical Myb proteins.

In this article, we focus on the typical R2R3 and R1R2R3 Myb proteins, which have sufficient sequence divergence to investigate molecular evolution of the Myb gene family. Recently, Dias et al. (2003) provided evidence for expansion of the maize R2R3 Myb gene family through genome duplication, tandem gene duplication, and a more ancient duplication. Additionally, Myb homologous genes in cotton appear to evolve independently in the allopolyploid nucleus, rather than via concerted evolution (Cedroni et al., 2003). However, the general evolutionary scenario of the Myb gene family still remains unclear; specifically, the ancient origin of the plant R2R3 Myb gene family is subject to controversy. Here, we analyzed new sorghum and maize Myb gene sequences obtained in our laboratory and available Myb sequence data to explore Myb gene evolutionary history, and to study the relationship of Myb gene sequences and their functional diversity.

Section snippets

Isolation and sequencing of Myb genes from sorghum and maize

Maize and sorghum Myb genes were isolated from Bacterial Artificial Chromosome (BAC) clones obtained from Clemson University Genomics Institute (CUGI), Clemson, South Carolina; www.genome.clemson.edu. Membrane filters containing arrayed clones of sorghum (SB_BBa) and maize (ZMMBBb) genomic libraries were hybridized with a radiolabeled fragment of a maize p1-wr gene cDNA containing a typical R2R3 Myb domain. Radiolabeled probes were prepared using an oligo-labeling kit (Amersham Pharmacia

Identification of Myb domains, conserved coding sequences and variant non-coding sequences in Myb genes

Currently there are relatively few complete Myb gene sequences available from cereal grain species. To increase the representation of Myb genes from these important crop plants, we isolated and sequenced maize and sorghum genes encoding Myb-homologous proteins. First, we isolated BAC clones that hybridized with a typical R2R3 Myb probe; second, we used a degenerate oligonucleotide primer complementary to a highly conserved region of Myb genes to sequence directly from each BAC clone. The

Expansion of Myb gene family in monocot

Previous reports have described the expansion of Myb-homologous genes in various plants including maize and Arabidopsis (e.g., Rabinowicz et al., 1999). For example, 125 R2R3 Myb genes have been identified in Arabidopsis (Stracke et al., 2001). Our results confirm and extend those studies, with new sequence data from 64 sorghum and 31 maize Myb genomic clones (accession numbers: F474125–AF474126AF474127AF474128AF474129AF474130AF474131AF474132AF474133AF470058–AF470059AF470060AF470061AF470062AF470063

Acknowledgements

We thank Terry Olson for the technical assistance in the isolation and sequencing of Myb genes. We acknowledge Monsanto/Pharmacia rice-research.org (www.rice-research.org) for providing the O. sativa genomic sequences. This work was supported by a grant from the USDA-NRICGP to T.P. and S.C, and an NIH grant to X. G. X.G is the Dupont young faculty. This is Journal Paper No. J-19751 of the Iowa Agriculture and Home Economics Experiment Station, Ames, IO, Project No. 3297, and supported by Hatch

References (31)

  • E.L. Braun et al.

    Newly discovered plant c-myb-like gene rewrite the evolution of the plant myb gene family

    Plant Physiol.

    (1999)
  • M.L. Cedroni et al.

    Evolution and expression of Myb genes in diploid and polyploid cotton

    Plant Mol. Biol.

    (2003)
  • K.C. Cone et al.

    Maize anthocyanin regulatory gene pl is a duplication of c1 that functions in the plant

    Plant Cell

    (1993)
  • A.P. Dias et al.

    Recently duplicated maize R2R3 Myb genes provide evidence for distinct mechanisms of evolutionary divergence after duplication

    Plant Physiol.

    (2003)
  • B.P. England et al.

    Cloning of Drosophila transcription factor Adf-1 reveals homology to Myb oncoproteins

    Proc. Natl. Acad. Sci. U. S. A.

    (1992)
  • Cited by (119)

    View all citing articles on Scopus
    1

    Present address: Department of Crop and Soil Science, Pennsylvania State University, University Park, PA 16802, USA.

    View full text