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Mining the Brassica oleracea Genome for Q-type C2H2 Zinc Finger Transcription Factor Genes

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Abstract

Q-type zinc finger proteins have been studied in several plant species and have been associated with response to stress. A whole genome analysis of Arabidopsis identified 176 putative C2H2 transcription factors (TF). Q-type C2H2 TFs containing the QALGGH motif and are a subset of these. In Arabidopsis, 18 have been described that contain two zinc finger motifs per protein, and several of these have been associated with a response to abiotic stress. The zinc fingers bind to the promoters of genes and negatively regulate transcription via the ethylene-responsive element-binding factor-associated amphiphilic repression (EAR) motif. Previously, we have identified StZFP2 from potato as induced upon infestation by insect pests. Interest in finding similar proteins in the newly annotated cabbage genome (Brassica oleracea var. capitata) led to the discovery of 25 proteins with 2-Q-type zinc finger domains. Examination of several transcriptome studies of B. oleracea submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) confirms the expression of all of these genes in at least one tissue type. Identification of the nearest homologs of these proteins in Arabidopsis and comparison of the map positions of both Arabidopsis and B. oleracea genes supports both the synteny between the genetic maps of these related species and the triplication event in Brassica species hypothesized to occur prior to the split from the ancestral progenitor of Arabidopsis and B. oleracea.

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Authors and Affiliations

  1. USDA-ARS, Invasive Insect Biocontrol and Behavior Lab, 10,300 Baltimore Ave. BARC-West, Bldg 007, Rm 301, Beltsville, MD, 20705, USA

    Susan D. Lawrence & Nicole G. Novak

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  1. Susan D. Lawrence
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  2. Nicole G. Novak
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Correspondence to Susan D. Lawrence.

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Fig. S1

Alignment of G1 proteins of the B. oleracea two fingered-Q-type C2H2 TFs. The zinc-finger domains are in red, the EAR motifs are in purple, the L-box is in blue and the B-box is in green (DOCX 14 kb)

Fig. S2

Alignment of G2 proteins of the B. oleracea Q-type two fingered C2H2 TFs. The zinc-finger domains are in red, the EAR motifs are in purple, the L-box is in blue and the B-box is in green (DOCX 14 kb)

Fig. S3

Alignment of Bol015615 with At1g49900. The zinc-finger domains are in red, the EAR motif is in purple and the B-box is in green. There are only two Q-type zinc finger domains in Bol015615 (DOCX 12 kb)

Fig. S4

Twenty Q-type two-fingered C2H2 TF B. oleracea genes map to a chromosome on the genome. The genes are similar to regions within blocks of the Arabidopsis genome. Genes containing similar proteins are indicated by arrows. The Q-type C2H2 TF is in bold. There is one 2i-B and one 2i-X-like protein found in the B. oleracea genome. Four 2i-C Arabidopsis proteins are similar to seven B. oleracea proteins. 5 mapped Arabidopsis 2i-D proteins are similar to 10 B. oleracea proteins. Finally, one outlier protein from B. oleracea is similar to a single 4i-A type protein from Arabidopsis (DOCX 37 kb)

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Lawrence, S.D., Novak, N.G. Mining the Brassica oleracea Genome for Q-type C2H2 Zinc Finger Transcription Factor Genes. Plant Mol Biol Rep 33, 1611–1617 (2015). https://doi.org/10.1007/s11105-015-0857-y

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