Genome-Wide Identification of Mitogen-Activated Protein Kinase Gene Family across Fungal Lineage Shows Presence of Novel and Diverse Activation Loop Motifs.

The mitogen-activated protein kinase (MAPK) is characterized by the presence of the T-E-Y, T-D-Y, and T-G-Y motifs in its activation loop region and plays a significant role in regulating diverse cellular responses in eukaryotic organisms. Availability of large-scale genome data in the fungal kingdom encouraged us to identify and analyse the fungal MAPK gene family consisting of 173 fungal species. The analysis of the MAPK gene family resulted in the discovery of several novel activation loop motifs (T-T-Y, T-I-Y, T-N-Y, T-H-Y, T-S-Y, K-G-Y, T-Q-Y, S-E-Y and S-D-Y) in fungal MAPKs. The phylogenetic analysis suggests that fungal MAPKs are non-polymorphic, had evolved from their common ancestors around 1500 million years ago, and are distantly related to plant MAPKs. We are the first to report the presence of nine novel activation loop motifs in fungal MAPKs. The specificity of the activation loop motif plays a significant role in controlling different growth and stress related pathways in fungi. Hence, the presences of these nine novel activation loop motifs in fungi are of special interest

Review of Andrew G. Newby, The Life and Times of Edward McHugh (1853-1915), Land Reformer, Trade Unionist, and Labour Activist (Lampeter, Lewiston, NY, and Queenston, Ontario: Edwin Mellen Press, 2004)

The details of phylogenetic datas are submitted to TreeBASE database and can be available in following link http://purl.org/phylo/treebase/phylows/study/TB2:S17414?x-access-code=1b88565e08ce238f8fc7928d2fa11a12&format=html

The phylogenetic tree of fungal MAPKs those contain a novel activation loop motif and all representative MAPKs of <i>A</i>. <i>thaliana</i> and <i>O</i>. <i>sativa</i>.

<p>The phylogenetic tree was constructed by taking all MAPKs of <i>O</i>. <i>sativa</i> and <i>A</i>. <i>thaliana</i> with MAPKs of fungi that contains only a “novel” activation loop motif [except one, i.e MbMPK (it contains a T-E-Y motif)]. The phylogenetic tree resulted into four different groups (red and lime color groups are plant-specific and magenta and blue colors are fungi-specific). OsMPKs and AtMPKs were grouped with AkMPK (T-T-Y motif) and AlMPK (T-I-Y motif) of fungi. This suggests that AkMPKs and AlMPKs which contains the T-T-Y and T-I-Y motifs can also be plant-specific as well, which is yet to be elucidated. The other MAPKs having T-N-Y, T-H-Y, T-S-Y, K-G-Y, T-Q-Y and S-E-Y activation loop motifs are those that fall into unique groups, which are specific to fungi only. The activation loop T-E-Y motif is very common and present in all three domains (plant, animal and fungi) of life. Therefore, one MAPK from fungi that contained the T-E-Y (MbMPK) motif was included in this study to better understand their grouping system and phylogenetic relationship. Owing to the presence of the T-E-Y motif, MbMPK is placed in between fungi and plant. Because the T-E-Y motif is common to all the three domains of life and others are unique to fungi, hence MbMPK is present in between the plant and fungi domains. ScMPK in the figure represents SLT2 of <i>Sachharomyces cerevisiae</i>.</p

Duplication and orthologous/paralogous analysis of S. <i>cerevisiae</i> MAPKs.

<p>(A) Duplication analysis shows, <i>S</i>. <i>cerevisiae</i> MAPKs are highly duplicated. The duplicated MAPKs are Fus3, Kss1, Hog1, 1519416 (uncharacterized) and Slt2 and non duplicated MAPK is Smk1. (B) Orthologous/paralogous gene analysis shows, except Smk1, all other MAPKs are orthologs. The analysis was done using Notung 2.6 software.</p

Tajima’s relative rate test.

<p>The equality of evolutionary rate analysis between sequences <b>A</b> (<i>OsMPK6</i>) and <b>B</b> (<i>ScMPK-A</i>), with sequence <b>C</b> (<i>CjMPK</i>) were used for the analysis of fungal MAPKs with a few AtMAPKs and OsMAPKs as the representative of T-E-Y and T-D-Y motifs. Sequences <b>A</b> (<i>DeMPK</i>) and <b>B</b> (<i>AtMPK1</i>), with sequence <b>C</b> (<i>CjMPK</i>) were used for fungal MAPKs with all the representative AtMAPKs and OsMAPKs as per default selection on the MEGA program. In the case of all fungal MAPKs that contain the novel activation loop motif, the equality of the evolutionary rate was calculated between sequences A (687684) and B (91669), with sequence C (5240). A <i>P</i>-value less than 0.05 is often used to reject the null hypothesis of equal rates between lineages. The analysis involved 3 amino acid sequences. All positions containing gaps and missing datas were eliminated. Evolutionary analyses were conducted in MEGA5.</p

Grouping of fungal MAPKs that contain the novel activation loop motif.

<p>The OsMAPKs (OsMPK6, OsMPK14) and AtMAPKs (AtMPK4 and AtMPK16) from four different MAPK groups (one sequence from each group) were taken to provide a proper grouping system to fungal MAPKs that contained the novel activation loop motif. The phylogenetic tree shows that MAPKs are grouped into four different groups. The fungal MAPKs, MbMPK (T-E-Y), DeMPK (T-G-Y), AkMPK (T-T-Y), AlMPK-A (T-I-Y) and ALMPK-B (S-E-Y) are grouped with OsMPK and AtMPK. This reflects that, the MAPKs with this novel activation loop motifs might also be present in plant kingdom too which are yet to be identified. ScMPK in the figure represents SLT2 of <i>Sachharomyces cerevisiae</i>.</p

The MAPK cascades in fungi.

<p>The Kss1 MAPK that regulates Kss1 pathway is responsible for filamentous growth contains T-E-Y motif in the activation loop domain. The Fus3 MAPK which responsible for mating and cell cycle arrest contains T-E-Y motif in its activation loop domain while Mpk1 which is responsible for cell wall remodeling, contains T-E-Y motif in the activation loop domain. The Hog1 which is responsible for hyperosmosis mediated glycerol synthesis contains T-G-Y motif. The Smk1 which regulates meiosis and sporulation pathway contains T-N-Y motif in the activation loop domain. This suggests that, different signaling pathways mediated by different fungal MAPKs are may be due to presence of different activation loop motifs. The activation loop motif play crucial role in mediating different signaling pathways in fungi.</p

Representative molecular structure of fungal MAPKs with their activation loop motifs.

<p>Different activation loop motifs shown in the figure are T-T-Y (AkMAPK), T-I-Y (AlMAPK-A), T-E-Y (CjMAPK), K-G-Y (ScMAPK-A), T-H-Y (LhMAPK), T-Q-Y (UrMAPK), T-G-Y (DeMAPK), T-N-Y (BiMAPK), T-S-Y (HvMAPK) and S-E-Y (AlMAPK-B). The items within the bracket represent MAPKs from different fungal species. The first letter represents the genus name in upper case, and the second letter represents the species name in lower case followed by MPK.</p