Publications

(**Corresponding author)

Simões I**, Voth DE**, Mota LJ**. (2022) Editorial: Obligate intracellular bacteria: Evasion and adaptative tactics shaping the host-pathogen interface. Front Cell Infect Microbiol. 2022 Jul 14;12:965554. doi: 10.3389/fcimb.2022.9655541

Martins-Marques T, Costa M, Catarino S, Simões I, Aasen T, Enguita F, Girao H (2022) Cx43-mediated sorting of miRNAs into extracellular vesicles. EMBO Reports e54312 DOI: 10.15252/embr.202154312

Matos AL, Curto P, Simões I.** (2022) Moonlighting in Rickettsiales: Expanding virulence landscape. Trop Med Infect Dis. 2022 Feb 19;7(2):32. doi: 10.3390/tropicalmed7020032.

Curto P, Barro A, Almeida C, Vieira-Pires RS, Simões I.** (2021) The retropepsin-type protease APRc as a novel Ig-binding protein and moonlighting immune evasion factor of Rickettsia. mBio. Dec 21;12(6):e0305921. doi: 10.1128/mBio.03059-21. Epub 2021 Dec 7.

Curto P, Santa C, Cortes L, Manadas B, Simões I**. (2021) Spotted fever group Rickettsia trigger species-specific alterations in macrophage proteome signatures with different impacts in host innate inflammatory responses. Microbiol Spectr. 2021 Dec 22;9(3):e0081421. doi: 10.1128/spectrum.00814-21. Epub 2021 Dec 22.

Figueiredo, P.R., Santos, S.F.G., Almeida, B.C., Simões, I.**, Carvalho, A.T.P.** (2021) Introduction of a glycine linker connecting the heavy and light chains in synthetic cardosin B-derived rennet changes the specificity of subpocket S3′. Journal of Physical Chemistry B, 2021, 125(17), pp. 4368–4374 10.1021/acs.jpcb.1c01826

Barracosa P., Simões I., Martins A.P., Barros M., Pires E. (2021) Biochemical diversity of cardoon flowers (Cynara cardunculus L.): Predicting PDO Mediterranean cheese textures. Food Bioscience Volume 39, doi.org/10.1016/j.fbio.2020.100805

Anjo, S., Simões I., Castanheira P., Grãos M., Manadas B. (2019) Use of recombinant proteins as a simple and robust normalization method for untargeted proteomics screening: exhaustive performance assessment. Talanta 205, 120163, doi.org/10.1016/j.talanta.2019.120163

Soares A., Niedermaier S., Faro R., Loos A., Manadas B., Faro C., Huesgen P.H.**, Cheung A.Y.**, Simões I.** (2019) An atypical aspartic protease modulates lateral root development in Arabidopsis thaliana. J. Exp Bot. Apr 12;70(7):2157-2171. doi: 10.1093/jxb/erz059.

Soares A., Ribeiro Carlton S.R., Simões I.** (2019) Atypical and nucellin-like aspartic proteases: emerging players in plant developmental processes and stress responses. J. Exp Bot. Apr 12;70(7):2059-2076. doi: 10.1093/jxb/erz034. Review

Curto P., Santa C., Allen P., Manadas B., Simões I.**, Martinez J.J.** (2019) A pathogen and a non-pathogen spotted fever group Rickettsia trigger differential proteome signatures in macrophages. Front Cell Infect Microbiol.9:43. doi: 10.3389/fcimb.2019.00043. eCollection 2019.

Curto P., Riley S.P., Simões I.**, Martinez J.J.** (2019) Macrophages infected by a pathogen and a non-pathogen spotted fever group Rickettsia reveal differential reprogramming signatures early in infection. Front Cell Infect Microbiol. 9:97. doi: 10.3389/fcimb.2019.00097. eCollection 2019.

Almeida C.M. & Simões I.** (2018) Cardoon-based rennets for cheese production. Appl Microbiol Biotechnol. https://doi.org/10.1007/s00253-018-9032-3 (Review)

Almeida C.M., Manso-Garcia J.A., Figueiredo A.C., Antunes L., Cruz R., Manadas B., Bur D., Barbosa Pereira P.J., Faro C., Simões I.**, (2017) Functional and structural characterization of synthetic cardosin B-derived rennet. Appl Microbiol Biotechnol. 101: 6951. https://doi.org/10.1007/s00253-017-8445-8

Curto P., Simões I., Riley S.P., Martinez J.J. (2016) Differences in intracellular fate of two spotted fever group Rickettsia species in macrophage-like cells. Front. Cell. Infect. Microbiol. 6:80, doi: 10.3389/fcimb.2016.00080.

Leal A.R., Cruz R., Bur D., Huesgen P.F., Faro, R., Manadas B., Wlodawer A., Faro C., Simões, I.** (2016) Enzymatic properties, evidence for in vivo expression, and intracellular localization of shewasin D, the pepsin homolog from Shewanella denitrificans. Scientific Reports, 6:23869, DOI: 10.1038/srep23869

Dias D.M., Furtado J., Wasielewski E., Cruz R., Costello B., Cole L., Faria T. Q., Baaske P., Brito R.M.M., Ciulli A., Simões I., Macedo-Ribeiro S., Faro C., Geraldes C. F. G. C., Castanheira P. (2016). Biophysical characterization of laforin-carbohydrate interaction. Biochemical J. 473, 335–345., DOI 10.1042/BJ20141555

Li M., Gustchina A., Cruz R., Simões M., Curto P., Martinez J., Faro C., Simões I.** & Wlodawer A.** (2015). Structure of RC1339/APRc from Rickettsia conorii, a retropepsin-like aspartic protease Acta Cryst. D71, 2109-2118 doi:10.1107/S1399004715013905

Malaquias Almeida C., Gomes D., Faro C., Simões I.** (2015) Engineering a cardosin B-derived rennet for sheep and goat cheese manufacture. Appl Microbiol Biotechnol. Jan;99(1):269-81. doi: 10.1007/s00253-014-5902-5.

Cruz R., Huesgen P., Riley S.P., Wlodawer A., Faro, C., Overall C. M., Martinez, J. J.** and Simões I.** (2014) RC1339/APRc from Rickettsia conorii is a novel aspartic protease with properties of retropepsin-like enzymes. PLoS Pathog. 10(8): e1004324. doi:10.1371/journal.ppat.1004324.

Curto P., Lufrano D., Pinto C., Custódio V., Gomes A.C., Trejo S., Bakás L., Vairo-Cavalli S., Faro C., and Simões I.** (2014) Establishing the yeast Kluyveromyces lactis as an expression host for production of the saposin-like domain (plant-specific insert) from the aspartic protease cirsin. Appl. Environ. Microbiol. January 80:1 86-96. doi: 10.1128/AEM.03151-13.

Resende R, Sueli C., Ferreiro BE., Simões I., Oliveira C., Pereira, C. (2013) Effect of a-synuclein on amyloid ß-induced toxicity. Relevance to Lewy Body variant of Alzheimer disease. Neurochemical Research DOI 10.1007/s11064-013-0982-7.

Lufrano D., Faro R., Castanheira P., Parisi G., Veríssimo P., Vairo-Cavalli S., Simões I.**, Faro C. (2012) Molecular cloning and characterization of procirsin, an active aspartic protease precursor from Cirsium vulgare (Asteraceae) Phytochemistry, Volume 81, 7–18, DOI:10.1016/j.phytochem.2012.05.028.

Almeida C. M., Pereira C., Costa D. S., Pereira S., Pissarra. J, Simões I., Faro C. (2012) Chlapsin, a chloroplastidial aspartic proteinase from the green algae Chlamydomonas reinhardtii. Planta. Volume 236, Number 1, 283-296, https://doi.org/10.1007/s00425-012-1605-2.

Simões I.**, Faro R.,Bur D., Kay J. and Faro, C. (2011) Shewasin A, an active pepsin homologue from the bacterium Shewanella amazonensis FEBS Journal, 278: 3177–3186. doi: 10.1111/j.1742-4658.2011.08243.x.

Simões I., Faro R., Bur D. and Faro C. (2007) Characterization of recombinant CDR1, an Arabidopsis aspartic proteinase involved in disease resistance. J. Biol. Chem., Vol. 282, Issue 43, 31358-31365. https://doi.org/10.1074/jbc.M702477200

Simões I., Mueller E.C., Otto A., Bur D., Cheung A.Y., Faro C., & Pires E. (2005) Molecular analysis of the interaction between cardosin A and phospholipase D(alpha). Identification of RGD/KGE sequences as binding motifs for C2 domains. FEBS J. 272, 5786-5798. https://doi.org/10.1111/j.1742-4658.2005.04967.x

Simões I. & Faro C. (2004) Structure and function of plant aspartic proteinases. Eur. J. Biochem. 271, 2067-2075 (Review). https://doi.org/10.1111/j.1432-1033.2004.04136.x

Faro C., Ramalho-Santos M.,Vieira M., Mendes A., Simões I., Andrade R., Veríssimo P., Lin X., Tang J. and Pires E. (1999) Cloning and characterization of cDNA encoding cardosin A, an RGD-containing plant aspartic proteinase. J. Biol. Chem. 274, 28724-28729. https://doi.org/10.1074/jbc.274.40.28724

Patents