Ghizal Siddiqui1, Amanda De Paoli1, Christopher A MacRaild1, Anna E Sexton1, Coralie Boulet2, Anup D Shah3,4, Mitchell B Batty1, Ralf B Schittenhelm3, Teresa G Carvalho2, Darren J Creek1. 1. Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia. 2. Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia. 3. Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia. 4. Monash Bioinformatics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
Abstract
BACKGROUND: Plasmodium falciparum causes the majority of malaria mortality worldwide, and the disease occurs during the asexual red blood cell (RBC) stage of infection. In the absence of an effective and available vaccine, and with increasing drug resistance, asexual RBC stage parasites are an important research focus. In recent years, mass spectrometry-based proteomics using data-dependent acquisition has been extensively used to understand the biochemical processes within the parasite. However, data-dependent acquisition is problematic for the detection of low-abundance proteins and proteome coverage and has poor run-to-run reproducibility. RESULTS: Here, we present a comprehensive P. falciparum-infected RBC (iRBC) spectral library to measure the abundance of 44,449 peptides from 3,113 P. falciparum and 1,617 RBC proteins using a data-independent acquisition mass spectrometric approach. The spectral library includes proteins expressed in the 3 morphologically distinct RBC stages (ring, trophozoite, schizont), the RBC compartment of trophozoite-iRBCs, and the cytosolic fraction from uninfected RBCs. This spectral library contains 87% of all P. falciparum proteins that have previously been reported with protein-level evidence in blood stages, as well as 692 previously unidentified proteins. The P. falciparum spectral library was successfully applied to generate semi-quantitative proteomics datasets that characterize the 3 distinct asexual parasite stages in RBCs, and compared artemisinin-resistant (Cam3.IIR539T) and artemisinin-sensitive (Cam3.IIrev) parasites. CONCLUSION: A reproducible, high-coverage proteomics spectral library and analysis method has been generated for investigating sets of proteins expressed in the iRBC stage of P. falciparum malaria. This will provide a foundation for an improved understanding of parasite biology, pathogenesis, drug mechanisms, and vaccine candidate discovery for malaria.
BACKGROUND: Plasmodium falciparum causes the majority of malaria mortality worldwide, and the disease occurs during the asexual red blood cell (RBC) stage of infection. In the absence of an effective and available vaccine, and with increasing drug resistance, asexual RBC stage parasites are an important research focus. In recent years, mass spectrometry-based proteomics using data-dependent acquisition has been extensively used to understand the biochemical processes within the parasite. However, data-dependent acquisition is problematic for the detection of low-abundance proteins and proteome coverage and has poor run-to-run reproducibility. RESULTS: Here, we present a comprehensive P. falciparum-infected RBC (iRBC) spectral library to measure the abundance of 44,449 peptides from 3,113 P. falciparum and 1,617 RBC proteins using a data-independent acquisition mass spectrometric approach. The spectral library includes proteins expressed in the 3 morphologically distinct RBC stages (ring, trophozoite, schizont), the RBC compartment of trophozoite-iRBCs, and the cytosolic fraction from uninfected RBCs. This spectral library contains 87% of all P. falciparum proteins that have previously been reported with protein-level evidence in blood stages, as well as 692 previously unidentified proteins. The P. falciparum spectral library was successfully applied to generate semi-quantitative proteomics datasets that characterize the 3 distinct asexual parasite stages in RBCs, and compared artemisinin-resistant (Cam3.IIR539T) and artemisinin-sensitive (Cam3.IIrev) parasites. CONCLUSION: A reproducible, high-coverage proteomics spectral library and analysis method has been generated for investigating sets of proteins expressed in the iRBC stage of P. falciparum malaria. This will provide a foundation for an improved understanding of parasite biology, pathogenesis, drug mechanisms, and vaccine candidate discovery for malaria.
Authors: David C Hondius; Pim van Nierop; Ka Wan Li; Jeroen J M Hoozemans; Roel C van der Schors; Elise S van Haastert; Saskia M van der Vies; Annemieke J M Rozemuller; August B Smit Journal: Alzheimers Dement Date: 2016-01-06 Impact factor: 21.566
Authors: Geoffrey W Birrell; Matthew P Challis; Amanda De Paoli; Dovile Anderson; Shane M Devine; Gavin D Heffernan; David P Jacobus; Michael D Edstein; Ghizal Siddiqui; Darren J Creek Journal: Mol Cell Proteomics Date: 2019-12-13 Impact factor: 5.911
Authors: Judith Straimer; Nina F Gnädig; Benoit Witkowski; Chanaki Amaratunga; Valentine Duru; Arba Pramundita Ramadani; Mélanie Dacheux; Nimol Khim; Lei Zhang; Stephen Lam; Philip D Gregory; Fyodor D Urnov; Odile Mercereau-Puijalon; Françoise Benoit-Vical; Rick M Fairhurst; Didier Ménard; David A Fidock Journal: Science Date: 2014-12-11 Impact factor: 47.728
Authors: Nina F Gnädig; Barbara H Stokes; Rachel L Edwards; Gavreel F Kalantarov; Kim C Heimsch; Michal Kuderjavy; Audrey Crane; Marcus C S Lee; Judith Straimer; Katja Becker; Ilya N Trakht; Audrey R Odom John; Sachel Mok; David A Fidock Journal: PLoS Pathog Date: 2020-04-20 Impact factor: 6.823
Authors: Carlo Giannangelo; Ghizal Siddiqui; Amanda De Paoli; Bethany M Anderson; Laura E Edgington-Mitchell; Susan A Charman; Darren J Creek Journal: PLoS Pathog Date: 2020-06-26 Impact factor: 6.823
Authors: Ghizal Siddiqui; Amanda De Paoli; Christopher A MacRaild; Anna E Sexton; Coralie Boulet; Anup D Shah; Mitchell B Batty; Ralf B Schittenhelm; Teresa G Carvalho; Darren J Creek Journal: Gigascience Date: 2022-03-07 Impact factor: 6.524
Authors: Rebecca C S Edgar; Ghizal Siddiqui; Katheryn Hjerrild; Tess R Malcolm; Natalie B Vinh; Chaille T Webb; Clare Holmes; Christopher A MacRaild; Hope C Chernih; Willy W Suen; Natalie A Counihan; Darren J Creek; Peter J Scammells; Sheena McGowan; Tania F de Koning-Ward Journal: Elife Date: 2022-09-13 Impact factor: 8.713
Authors: Coralie Boulet; Ghizal Siddiqui; Taylah L Gaynor; Christian Doerig; Darren J Creek; Teresa G Carvalho Journal: Microorganisms Date: 2022-04-15