Proteome Regulation in Plants Lab

	Isabel Abreu
	Principal Investigator
	abreu@itqb.unl.pt
	Proteome Regulation in Plants Laboratory

Current members
Cleverson Matiolli	Post-Doc Researcher
Ana Sofia Fortunato	Post-Doc Researcher
Inês Luís	PhD student
Telma Fernandes	PhD student
Hugo Alves	PhD student
Joana Marques	PhD student
Rafael Soares	PhD student
Ana Gonçalves	PhD student

Current Projects
2022-2025 \| FilliGRAIN-PROTECT – Using the power of plant signal-integration to protect grain filling from stress (PTDC/ASP-PLA/1920/202) Principal Investigator: Isabel Abreu
2022 – 2025 \| The BioPlaTTAR Platform for the Tailored and Rapid Development of Antiviral Biopharmaceuticals (HR22-00722/2022). Coordinator: Cláudio Soares (ITQB NOVA)
2021-2024 \| Heat stress during the progamic phase: Impact on male gametophytes of angiosperms at transcriptome and proteome level (PTDC/ASP-PLA/2007/2020) Principal Investigator: Jörg Becker
2021-2024 \| Impact of ABA signalling on plant growth regulatory pathways and root architecture (PTDC/BIA-FBT/4942/2020) Principal Investigator: Elena Baena
2021-2023 \| Genomics and Metabolomics in a Host-Microbe Symbiosis Network - SymbNET (WIDESPREAD-05-2020 – Twinning no. 952537)
2020-2023 \| PhotoBoost. A holistic approach to improve the photosynthetic performance and productivity of C3 crops under diverse environmental conditions (H2020-NMBP-BIO-2019) Grant agreement ID: 862127
	2020-2024 \| "TRACE RICE” - Tracing rice and valorizing side streams along mediterranean blockchain" (H2020 - PRIMA Programme - Partnership for research and innovation in the Mediterranean Area) (Grant nº 1934). Project Coordinator: Carla Brites (INIAV)
2018-2022 \| Growth-Stress NET: Building new regulatory networks governing plant growth under stress (PTDC/BIA-FBT/31211/2017 ) Principal Investigator: Isabel Abreu
2018-2022 \| Metals in the radiation resistance bacterium Deinococcus radiodurans, its role in protection up to future applications (PTDC/BIA-BQM/31317/2017)

Past Projects

2014-2017 | Control of abiotic stress responses by the plant DELLAs and chemicals stabilizing these repressors. Plant-KBBE DELLA-STRESS (P-KBBE/0001/2012)

2012-2016 | (3to4): Converting C3 to C4 photosynthesis for sustainable agriculture. EU FP7 (KBBE.2011.3.1‐01)

2012-2015 | SuberStress - An integrated approach to identify stress-related regulatory genes in cork oak (PTDC/AGR-GPL/118505/2010)

2013-2015 | SUMOdulator - Researching SUMO modulation of plant abiotic stress responses”. PTDC/BIA-PLA/3850/2012

2013-2014 | GENOSUBER: Sequencing the Cork Oak genome

2010-2013 | Oxidative stress response mechanisms in Deinococcus radiodurans” (PTDC/QUI-BIQ/100007/2008)

Main selected publications

2022

MARQUES J; Matiolli CC, Abreu IA. (2022), Visualization of a curated Oryza sativa L. CDPKs Protein-Protein Interaction Network (CDPK-OsPPIN). microPublication Biology. DOI: 10.17912/micropub.biology.000513.

2021

MATIOLLI CC, Soares RC, Alves HL, Abreu IA (2021) Turning the knobs: The impact of post-translational modifications on carbon metabolism. Front. Plant Sci. 12:781508. DOI: 10.3389/fpls.2021.781508

LOBATO M, Huang X, Alvarez D, He W, Baysal C, Zhu C, Armario-Najera V,Blanco Perera A, Cerda P, Saba A, Sobrino GM, Abranches R, Abreu IA, Balamurugan S, Bock R, Buyel JF, da Cunha NB, Daniel H, Faller R, Folgado A, Gowtham I, Häkkinen ST, Khan I, Kumar RS, Lacorte C, Lomonossoff GP, Luís IM, Ma JKC, McDonald KA, Murad A, Nandi S, O’Keef B, Oksman-Caldentey K-M, Parthiban S, Paul MJ, Ponndorf D, Rech E, Rodrigues JCM, Ruf S, Schillberg S, Schwestka J, Shah PS, Singh R, Stoger E, Twyman RM, Varghese IP. Vianna GR, Webster G, Wilbers RHP, Capell T, Christou P (2021) Contributions of the international plant science community to the fight against infectious diseases in humans – part 1: epidemic and pandemic diseases, including HIV/AIDS and coronaviruses. Accepted at Plant Biotechnology Journal.

LOBATO M, Huang X, Alvarez D, He W, Baysal C, Zhu C, Armario-Najera V,Blanco Perera A, Cerda P, Saba A, Sobrino GM, Abranches R, Abreu IA, Balamurugan S, Bock R, Buyel JF, da Cunha NB, Daniel H, Faller R, Folgado A, Gowtham I, Häkkinen ST, Khan I, Kumar RS, Lacorte C, Lomonossoff GP, Luís IM, Ma JKC, McDonald KA, Murad A, Nandi S, O’Keef B, Oksman-Caldentey K-M, Parthiban S, Paul MJ, Ponndorf D, Rech E, Rodrigues JCM, Ruf S, Schillberg S, Schwestka J, Shah PS, Singh R, Stoger E, Twyman RM, Varghese IP. Vianna GR, Webster G, Wilbers RHP, Capell T, Christou P (2021) Contributions of the international plant science community to the fight against infectious diseases in humans –part 2: endemic and re-emerging diseases. Accepted at Plant Biotechnology Journal

ALVES HLS, Matiolli CC, Soares RC, Almadanim MC, Oliveira MM, Abreu IA (2021) Carbon metabolism and stress response networks – CDPKs as the missing link? Accepted at Journal of Experimental Botany as a Darwin Review.

Other Selected Publications

GONÇALVES NG, Fernandes T, Nunes C, Rosa MTG, Matiolli CC, Rodrigues MAA, Barros PM, Oliveira MM, Abreu IA (2020) SUMOylation of rice DELLA SLR1 modulates transcriptional responses and improves yield under salt stress. Submitted to Plant Physiol, at BioRxiv doi: 10.1101/2020.03.10.986224.

SANTOS SP, Yang Y, Rosa MTG, Rodrigues MAA, De La Tour CB, Sommer S, Teixeira M, Carrondo MA, Cloetens P, Abreu IA*, Romão CM (2019) The interplay between Mn and Fe in Deinococcus radiodurans triggers cellular protection during paraquat-induced oxidative stress. Scientific Reports volume 9, Article number: 17217.

BOVDILOVA A, Alexandre BM, Höppner A, Matias Luís I, Alvarez CE, Bickel D, Gohlke H, Decker C, Nagel-Steger L, Alseekh S, Fernie AR, Drincovich MF, Abreu IA, Maurino VG. (2019) Posttranslational modification of the NADP-malic enzyme involved in C4 photosynthesis fine-tunes the enzymatic activity during the day. The Plant Cell. 31:2525-2539. doi: 10.1105/tpc.19.00406.

GOMES RA, Almeida C, Correia C, Guerreiro A, Simplício AL, Abreu IA, Alves PG (2019) Exploring the analytical power of the QTOF MS platform to assess monoclonal antibodies quality attributes. PLoS One. 2019 Jul 10;14:e0219156. doi: 10.1371/journal.pone.0219156. eCollection 2019.

ROSA MTG and Abreu IA (2019) Exploring the regulatory levels of SUMOylation to increase crop productivity. Curr Opin Plant Biol. 49:43-51. doi: 10.1016/j.pbi.2019.04.009.

ESCANDELL JM, Carvalho ESM, Gallo-Fernandez M, Reis C, Matmati S, Luis IM, Abreu IA, Coulon S, Ferreira MG (2019) SSU72 phosphatase is a telomere replication terminator. EMBO J. 38(7),e100476. doi: 10.15252/embj.2018100476

TEIXEIRA S, Luís IM, Oliveira MM, Abreu IA, Batista R (2019) Goji berries superfood – contributions for the characterization of proteome and IgE-binding proteins. Food and Agricultural Immunology. 30:262-280.

ROSA MTG, Almeida DM, Pires IS, Farias DR, Martins AG, Maia LC, Costa de Oliveira A, Saibo NJM, Oliveira MM and Abreu IA (2018) Insights into the transcriptional and post-transcriptional regulation of the rice SUMOylation machinery and into the role of two rice SUMO proteases. BMC Plant Biology. 18:349. doi:10.1186/s12870-018-1547-3.

RAMOS AM, Usié A, Barbosa P, Barros PM, Capote T, Chaves I, Simões F, Abreu IA, Carrasquinho I, Faro C, Guimarães JB, Mendonça D, Nóbrega F, Rodrigues L, Saibo NJM, Varela MC, Egas C, Matos J, Miguel CM, Oliveira MM, Ricardo CP, Gonçalves S. (2018) The draft genome sequence of cork oak. Sci Data. May 22;5:180069. doi: 10.1038/sdata.2018.69

BORBA AR, Serra TS, Górska A, Gouveia P, Cordeiro AM, Reyna-Llorens I, Knerová J, Barros PM, Abreu IA, Oliveira MM, Hibberd JM, Saibo NJM. (2018) Synergistic binding of bHLH transcription factors to the promoter of the maize NADP-ME gene used in C4 photosynthesis is based on an ancient code found in the ancestral C3 state. Mol Biol Evol. 35:1690-1705. doi: 10.1093/molbev/msy060

ALMADANIM MC, Gonçalves NM, Rosa MT, Alexandre BM, Cordeiro AM, Rodrigues M, Saibo NJM, Soares CM, Romão CV, Oliveira MM, Abreu IA (2018) The rice cold-responsive calcium-dependent protein kinase OsCPK17 is regulated by alternative splicing and post-translational modifications. Biochim Biophys Acta. 1865:231-246. doi: 10.1016/j.bbamcr.2017.10.010

ALMADANIM MC, Alexandre BM, Rosa MT, Sapeta H, Leitão AE, Ramalho JC, Lam TT, Negrão S, Abreu IA*, Oliveira MM (2017) Rice calcium-dependent protein kinase OsCPK17 targets plasma membrane intrinsic protein and sucrose phosphate synthase and is required for a proper cold stress response. Plant Cell Environ. 40:1197-1213. doi: 10.1111/pce.12916

LUÍS IM, Alexandre BM, Oliveira MM, Abreu IA (2016) Selection of an appropriate protein extraction method to study the phosphoproteome of maize photosynthetic tissue. PLOS ONE. 11: e0164387. doi: 10.1371/journal.pone.0164387

ALMEIDA D.*, Abreu IA*, Matos CA, Fraga J, Fernandes S, Macedo MA, Gutiérrez-Gallego R, Pereira PJ, Carvalho AL, Macedo Ribeiro S (2015) SUMOylation of the brain-predominant Ataxin-3 isoform modulates its interaction with p97. BBA - Mol. Basis of Disease 1852:1950-1959

Current Projects
2022-2025 \| FilliGRAIN-PROTECT – Using the power of plant signal-integration to protect grain filling from stress (PTDC/ASP-PLA/1920/202) Principal Investigator: Isabel Abreu
2022 – 2025 \| The BioPlaTTAR Platform for the Tailored and Rapid Development of Antiviral Biopharmaceuticals (HR22-00722/2022). Coordinator: Cláudio Soares (ITQB NOVA)
2021-2024 \| Heat stress during the progamic phase: Impact on male gametophytes of angiosperms at transcriptome and proteome level (PTDC/ASP-PLA/2007/2020) Principal Investigator: Jörg Becker
2021-2024 \| Impact of ABA signalling on plant growth regulatory pathways and root architecture (PTDC/BIA-FBT/4942/2020) Principal Investigator: Elena Baena
2021-2023 \| Genomics and Metabolomics in a Host-Microbe Symbiosis Network - SymbNET (WIDESPREAD-05-2020 – Twinning no. 952537)
2020-2023 \| PhotoBoost. A holistic approach to improve the photosynthetic performance and productivity of C3 crops under diverse environmental conditions (H2020-NMBP-BIO-2019) Grant agreement ID: 862127
	2020-2024 \| "TRACE RICE” - Tracing rice and valorizing side streams along mediterranean blockchain" (H2020 - PRIMA Programme - Partnership for research and innovation in the Mediterranean Area) (Grant nº 1934). Project Coordinator: Carla Brites (INIAV)
2018-2022 \| Growth-Stress NET: Building new regulatory networks governing plant growth under stress (PTDC/BIA-FBT/31211/2017 ) Principal Investigator: Isabel Abreu
2018-2022 \| Metals in the radiation resistance bacterium Deinococcus radiodurans, its role in protection up to future applications (PTDC/BIA-BQM/31317/2017)