Qi Yi, Kuang Di, Kelley Kylan, Buchser William J, Hinton Shantá D
Department of Biology, Integrated Science Center, College of William and Mary, 540 Landrum Drive, Williamsburg, VA, 23185, USA.
Department of Genetics, Washington University, St. Louis, MO, 63110, USA.
Sci Rep. 2022 Mar 9;12(1):4139. doi: 10.1038/s41598-022-07943-5.
The dual specificity phosphatase (DUSP) family has catalytically inactive members, called pseudophosphatases. They have mutations in their catalytic motifs that render them enzymatically inactive. This study analyzes the significance of two pseudophosphatases, MK-STYX [MAPK (mitogen-activated protein kinase phosphoserine/threonine/tyrosine-binding protein]) and STYX (serine/threonine/tyrosine-interacting protein), throughout their evolution and provides measurements and comparison of their evolutionary conservation. Phylogenetic trees were constructed to show any deviation from various species evolutionary paths. Data was collected on a large set of proteins that have either one of the two domains of MK-STYX, the DUSP domain or the cdc-25 homology (CH2) /rhodanese-like domain. The distance between species pairs for MK-STYX or STYX and Ka/Ks ratio were calculated. In addition, both pseudophosphatases were ranked among a large set of related proteins, including the active homologs of MK-STYX, MKP (MAPK phosphatase)-1 and MKP-3. MK-STYX had one of the highest species-species protein distances and was under weaker purifying selection pressure than most proteins with its domains. In contrast, the protein distances of STYX were lower than 82% of the DUSP-containing proteins and was under one of the strongest purifying selection pressures. However, there was similar selection pressure on the N-terminal sequences of MK-STYX, STYX, MKP-1, and MKP-3. We next perform statistical coupling analysis, a process that reveals interconnected regions within the proteins. We find that while MKP-1,-3, and STYX all have 2 functional units (sectors), MK-STYX only has one, and that MK-STYX is similar to MKP-3 in the evolutionary coupling of the active site and KIM domain. Within those two domains, the mean coupling is also most similar for MK-STYX and MKP-3. This study reveals striking distinctions between the evolutionary patterns of MK-STYX and STYX, suggesting a very specific role for each pseudophosphatase, further highlighting the relevance of these atypical members of DUSP as signaling regulators. Therefore, our study provides computational evidence and evolutionary reasons to further explore the properties of pseudophosphatases, in particular MK-STYX and STYX.
双特异性磷酸酶（DUSP）家族中有一些催化无活性的成员，称为假磷酸酶。它们在催化基序中存在突变，使其失去酶活性。本研究分析了两种假磷酸酶MK-STYX[丝裂原活化蛋白激酶（MAPK）磷酸丝氨酸/苏氨酸/酪氨酸结合蛋白]和STYX（丝氨酸/苏氨酸/酪氨酸相互作用蛋白）在整个进化过程中的重要性，并对它们的进化保守性进行了测量和比较。构建了系统发育树以显示与各种物种进化路径的任何偏差。收集了大量具有MK-STYX的两个结构域之一（DUSP结构域或cdc-25同源性（CH2）/硫氧还蛋白样结构域）的蛋白质的数据。计算了MK-STYX或STYX的物种对之间的距离以及Ka/Ks比率。此外，这两种假磷酸酶在大量相关蛋白质中进行了排名，包括MK-STYX的活性同源物MKP（MAPK磷酸酶）-1和MKP-3。MK-STYX具有最高的物种间蛋白质距离之一，并且与其结构域的大多数蛋白质相比，处于较弱的纯化选择压力之下。相比之下，STYX的蛋白质距离低于82%的含DUSP蛋白质，并且处于最强的纯化选择压力之一。然而，MK-STYX、STYX、MKP-1和MKP-3的N端序列存在相似的选择压力。接下来，我们进行了统计耦合分析，这一过程揭示了蛋白质内的相互连接区域。我们发现，虽然MKP-1、-3和STYX都有2个功能单元（区域），但MK-STYX只有1个，并且在活性位点和KIM结构域的进化耦合方面，MK-STYX与MKP-3相似。在这两个结构域内，MK-STYX和MKP-3的平均耦合也最为相似。这项研究揭示了MK-STYX和STYX进化模式之间的显著差异，表明每种假磷酸酶都有非常特定的作用，进一步突出了这些非典型DUSP成员作为信号调节因子的相关性。因此，我们的研究提供了计算证据和进化原因，以进一步探索假磷酸酶的特性，特别是MK-STYX和STYX。
