Genome-Wide Analysis of the Zn(II)₂Cys₆ Zinc Cluster-Encoding Gene Family in Tolypocladiumguangdongense and Its Light-Induced Expression

Abstract

The Zn(II)₂Cys₆ zinc cluster gene family is a subclass of zinc-finger proteins, which are transcriptional regulators involved in a wide variety of biological processes in fungi. We performed genome-wide identification and characterization of Zn(II)₂Cys₆ zinc-cluster gene (C6 zinc gene) family in Tolypocladiumguangdongense, Cordycepsmilitaris and Ophiocordycepssinensis. Based on the structures of the C6 zinc domains, these proteins were observed to be evolutionarily conserved in ascomycete fungi. We focused on T.guangdongense, a medicinal fungus, and identified 139 C6 zinc genes which could be divided into three groups. Among them, 49.6% belonged to the fungal specific transcriptional factors, and 16% had a DUF3468 domain. Homologous and phylogenetic analysis indicated that 29 C6 zinc genes were possibly involved in the metabolic process, while five C6 zinc genes were supposed to be involved in asexual or sexual development. Gene expression analysis revealed that 54 C6 zinc genes were differentially expressed under light, including two genes that possibly influenced the development, and seven genes that possibly influenced the metabolic processes. This indicated that light may affect the development and metabolic processes, at least partially, through the regulation of C6 zinc genes in T.guangdongense. Our results provide comprehensive data for further analyzing the functions of the C6 zinc genes.

Keywords: C6 zinc gene; Cordyceps; expression pattern; fruiting body development; metabolic process.

Figure 1

Estimates of C6 zinc genes and fungal specific transcription factors (FS-TFs) in Tolypocladium guangdongense, Cordyceps militaris and Ophiocordyceps sinensis genomes by automatic and manual analyses. The detail information was shown in Table S2.

Figure 2

Classification of the identified C6 zinc proteins in T. guangdongense (CCG), C. militaris (CCM) and O. sinensis (OCS).

Figure 3

Genomic distribution of C6 zinc domain genes in T. guangdongense. 139 genes are located on six chromosomes. The numbers at the right side of the chromosomal bar indicate the names of C6 zinc domain genes and the corresponding position on the chromosome (megabase pairs; Mb) are given in Table S4. The “SM000906” type genes are represented in pink, “PF04082” type genes are in blue, “PF11951” type genes are in green and other “SM00066” type genes are in yellow color.

Figure 4

Phylogenetic relationship of 34 DUF3468 domain contained C6 zinc proteins in T. guangdongense. Amino acid sequences were aligned using ClustalW, and phylogenetic tree were generated by the neighbor-joining (NJ) method using MEGA 5.0. Numbers at the branch point of the node represent the value resulting from 1000 replications. All positions with less than 50% site coverage were eliminated. CCG, T. guangdongense; CCM, C. militaris; Sm, S. macrospora; Nc, N. crassa; An, A. nidulans; Os, O. sinensis; Af, Aspergillus flavus. GenBank numbers of other proteins are listed as follows: OsPRO1A, EQL03797; NcPRO1A, CAC86433; AnRosA, CAD58393; CCM_02062, XP_006667279; AnsfgA, AAY99779; SmPRO1, CAB52588; NCPRO1, AJ238440; AnNosA, CAJ76908; AfaswA, XP_002373431; CCM_02196, XP_006667411.

Figure 5

Conserved motifs in the DUF3468 domain contained C6 zinc proteins. Ten conserved motifs in all proteins were identified through the multiple EM for motif elicitation (MEME) analysis and were indicated in different colored boxes. CCG, T. guangdongense; CCM, C. militaris; Sm, S. macrospora; Nc, N. crassa; An, A. nidulans; Os, O. sinensis; Af, Aspergillus flavus. GenBank numbers of the related proteins are the same as Figure 4. Scale bar indicates a number of amino acids (aa). For details of motifs refer to Table S6 and Figure S2.

Figure 6

Expression profiles of C6 zinc domain genes under different light conditions in T. guangdongense. (A), Expression patterns of differentially expressed genes; (B), Gene classification based on the Expression patterns. Type 1 represented genes immediately increased expression levels after light treatment. Type 2 represented genes immediately decreased expression levels after light treatment. Type 3 represented genes showing no change in expression levels when light treatment for 30 min, but increased firstly and then stabilized expression pattern after light treatment for 30 min. Type 4 represented genes showing no change in expression levels when light treatment for 30 min, but increased firstly and then returned to the starting level after light treatment for 30 min. Type 5 represented gene showing no change in expression levels at first, but up-regulation after light treatment for four hours. Type 6 represented genes showing no change in expression levels when light treatment for 30 min, but decreased firstly and then returned to the starting level after light treatment for 30 min. Type 7 represented gene showing no change in expression levels at first, but down-regulation after light treatment for four hours.

Figure 7

Expression levels of C6 zinc domain genes under different light conditions in T. guangdongense. The heatmap was constructed based on the FPKM values of C6 zinc domain genes. Genes immediately up-regulated by light are represented in pink, and immediately down-regulated by light are represented in yellow. Genes up-regulated by light after treatment for more than four hours are represented in blue.