@article{HansenMeyerFerrarietal.2017,
  author    = {Hansen, Bjoern Oest and Meyer, Etienne H. and Ferrari, Camilla and Vaid, Neha and Movahedi, Sara and Vandepoele, Klaas and Nikoloski, Zoran and Mutwil, Marek},
  title     = {Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana},
  series = {New phytologist : international journal of plant science},
  volume    = {217},
  journal   = {New phytologist : international journal of plant science},
  number    = {4},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0028-646X},
  doi       = {10.1111/nph.14921},
  pages     = {1521 -- 1534},
  year      = {2017},
  abstract  = {Recent advances in gene function prediction rely on ensemble approaches that integrate results from multiple inference methods to produce superior predictions. Yet, these developments remain largely unexplored in plants. We have explored and compared two methods to integrate 10 gene co-function networks for Arabidopsis thaliana and demonstrate how the integration of these networks produces more accurate gene function predictions for a larger fraction of genes with unknown function. These predictions were used to identify genes involved in mitochondrial complex I formation, and for five of them, we confirmed the predictions experimentally. The ensemble predictions are provided as a user-friendly online database, EnsembleNet. The methods presented here demonstrate that ensemble gene function prediction is a powerful method to boost prediction performance, whereas the EnsembleNet database provides a cutting-edge community tool to guide experimentalists.},
  language  = {en}
}
@article{PandeyYuOmranianetal.2019,
  author    = {Pandey, Prashant K. and Yu, Jing and Omranian, Nooshin and Alseekh, Saleh and Vaid, Neha and Fernie, Alisdair R. and Nikoloski, Zoran and Laitinen, Roosa A. E.},
  title     = {Plasticity in metabolism underpins local responses to nitrogen in Arabidopsis thaliana populations},
  series = {Plant Direct},
  volume    = {3},
  journal   = {Plant Direct},
  number    = {11},
  publisher = {John Wiley \& sonst LTD},
  address   = {Chichester},
  issn      = {2475-4455},
  doi       = {10.1002/pld3.186},
  pages     = {6},
  year      = {2019},
  abstract  = {Nitrogen (N) is central for plant growth, and metabolic plasticity can provide a strategy to respond to changing N availability. We showed that two local A. thaliana populations exhibited differential plasticity in the compounds of photorespiratory and starch degradation pathways in response to three N conditions. Association of metabolite levels with growth-related and fitness traits indicated that controlled plasticity in these pathways could contribute to local adaptation and play a role in plant evolution.},
  language  = {en}
}
@article{JanowskiZoschkeScharffetal.2018,
  author    = {Janowski, Marcin Andrzej and Zoschke, Reimo and Scharff, Lars B. and Jaime, Silvia Martinez and Ferrari, Camilla and Proost, Sebastian and Xiong, Jonathan Ng Wei and Omranian, Nooshin and Musialak-Lange, Magdalena and Nikoloski, Zoran and Graf, Alexander and Schoettler, Mark Aurel and Sampathkumar, Arun and Vaid, Neha and Mutwil, Marek},
  title     = {AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome},
  series = {The plant journal},
  volume    = {96},
  journal   = {The plant journal},
  number    = {2},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0960-7412},
  doi       = {10.1111/tpj.14040},
  pages     = {404 -- 420},
  year      = {2018},
  abstract  = {Plastid ribosomes are very similar in structure and function to the ribosomes of their bacterial ancestors. Since ribosome biogenesis is not thermodynamically favorable under biological conditions it requires the activity of many assembly factors. Here we have characterized a homolog of bacterial RsgA in Arabidopsis thaliana and show that it can complement the bacterial homolog. Functional characterization of a strong mutant in Arabidopsis revealed that the protein is essential for plant viability, while a weak mutant produced dwarf, chlorotic plants that incorporated immature pre-16S ribosomal RNA into translating ribosomes. Physiological analysis of the mutant plants revealed smaller, but more numerous, chloroplasts in the mesophyll cells, reduction of chlorophyll a and b, depletion of proplastids from the rib meristem and decreased photosynthetic electron transport rate and efficiency. Comparative RNA sequencing and proteomic analysis of the weak mutant and wild-type plants revealed that various biotic stress-related, transcriptional regulation and post-transcriptional modification pathways were repressed in the mutant. Intriguingly, while nuclear- and chloroplast-encoded photosynthesis-related proteins were less abundant in the mutant, the corresponding transcripts were increased, suggesting an elaborate compensatory mechanism, potentially via differentially active retrograde signaling pathways. To conclude, this study reveals a chloroplast ribosome assembly factor and outlines the transcriptomic and proteomic responses of the compensatory mechanism activated during decreased chloroplast function. Significance Statement AtRsgA is an assembly factor necessary for maturation of the small subunit of the chloroplast ribosome. Depletion of AtRsgA leads to dwarfed, chlorotic plants, a decrease of mature 16S rRNA and smaller, but more numerous, chloroplasts. Large-scale transcriptomic and proteomic analysis revealed that chloroplast-encoded and -targeted proteins were less abundant, while the corresponding transcripts were increased in the mutant. We analyze the transcriptional responses of several retrograde signaling pathways to suggest the mechanism underlying this compensatory response.},
  language  = {en}
}