Phytophthora capsici is a phytopathogenic oomycete
Phytophthora capsici is a phytopathogenic oomycete, a lineage of eukaryotic microorganisms in the kingdom Stramenopila, which causes devastating diseases on many economically important vegetables . Hyps are present in the Phytophthora cell wall proteins  and phytotoxic elicitor proteins . The rapid rhammification of hyphae through leafy tissues is likely associated with localized regions of hypoxia, and thus, the hydroxylation of transcription factors or other regulatory proteins, which could mediate abrupt changes in expression patterns. In this study, we searched on P. capsici genome to find five genes encoding P4H-like polypeptides. Then we tested expression patterns of these PcP4Hs and crystal structure of PcP4H1 to learn more about their biological roles in oomycetes.
Material and methods
Discussion The putative five P. capsici P4Hs can be clustered into three clades, with PcP4H1, PcP4H2 and PcP4H3 being the most divergent members. PcP4H1 expression level was strongly downregulated in response to hypoxic conditions, but upregulated more than 110-fold with 90 min after leaf inoculation. The responsiveness of PcP4H1 to hypoxia and infection, and its predicted function as a protein modifying enzyme, hint that it could be a key virulence driver protein, analogous to the role played by oncogenes in cancer. The transcript abundance of other PcP4Hs were all transiently lower in response to hypoxia, but had differential responses during infection indicating that they might play various roles in different physiological processes in Phytophthora. Structural comparison of PcP4H1 with PPHD and human HIF1α-PHD2 reveals that DSBH core fold, Fe2+ and 2-oxoglutarate so much are all conserved. The low affinity of PcP4H1 for 2-oxyglutarate (550 mM) relative to the K value of 2-oxoglutarate for PPHD (400 μM)  suggests that other molecules may function as the cofactor. The Cys150-Cys285 disulfide bridge led the α9-helix connects to the DSBH to stabilize it and rigidify the catalytic βⅡ-βⅢ loop. A similar disulfide bridge is present in CrP4H-1 crystal structure . The putative substrate binding β2-β3 loop in PcP4H1 is composed of residues 65–96 and much longer than that of other P4Hs (residues 51-74PPHD, residues 236–258PHD2 and residues 76–99 CrP4H-1). The PcP4H1 βII-βIII thumb loop has similar length and location as those of P4Hs. The extended C-terminal might affect the substrate specificity. Considering different polypeptide substrates adopt similar conformations when bound to their respective P4Hs, we propose that PcP4H1 is a PHD2-like hydroxylase binding to specific peptide substrate in a similar conformation. The structure information of PcP4H1 may provide insight into molecular understanding of hypoxic response and PHDs inhibitor design.
Conflicts of interest
Acknowledgements We thank the Shanghai Synchrotron Radiation Facility SSRF, China for providing the synchrotron-radiation facilities and the staff of beamlines BL18U1 and BL19U1 for their assistance in the data collection. The work was supported by Earmarked Fund for China Agriculture Research System (CARS-25-03B).
Introduction The extracellular matrix (ECM) is essential for the molecular mechanisms that determine cell survival, differentiation and movement in all multicellular organisms . Cells in tissues are structurally and functionally integrated with their surrounding ECM through dynamic connections. The ECM harbors a remarkable versatility of organization in tissues that is supported by a relatively small set of structural proteins encoded by ∼300 genes in vertebrates [2,3]. But the ECM, as defined by the matrisome , contains another category of proteins: the matrisome-associated proteins. The latter category encompasses the ECM regulators such as the matrix enzymes and represents no fewer than two thirds of the entire matrisome. The ECM regulators as well as the ECM secreted factors (e.g. growth factors and cytokines) can fine-tune ECM activities in a narrow window of time and thereby confer to them additional functions in a given tissue. How ECM molecules assemble to form organized tissues and how crucial interactive domains within ECM proteins are structurally organized to allow network formation or signaling through cellular receptor recognition remain important questions that are far from being fully addressed. It is particularly true for the collagen superfamily that contains large multi-domain proteins and are often expressed ubiquitously in tissues .