Proteomes of an oxygenic photosynthetic cyanobacterium, Synechocystis sp. PCC 6803, were analyzed... more Proteomes of an oxygenic photosynthetic cyanobacterium, Synechocystis sp. PCC 6803, were analyzed under photoautotrophic (low and high CO2, assigned as ATLC and ATHC), photomixotrophic (MT), and light-activated heterotrophic (LAH) conditions. Allocation of proteome mass fraction to seven sub-proteomes and differential expression of individual proteins were analyzed, paying particular attention to photosynthesis and carbon metabolism–centered sub-proteomes affected by the quality and quantity of the carbon source and light regime upon growth. A distinct common feature of the ATHC, MT, and LAH cultures was low abundance of inducible carbon-concentrating mechanisms and photorespiration-related enzymes, independent of the inorganic or organic carbon source. On the other hand, these cells accumulated a respiratory NAD(P)H dehydrogenase I (NDH-11) complex in the thylakoid membrane (TM). Additionally, in glucose-supplemented cultures, a distinct NDH-2 protein, NdbA, accumulated in the TM, ...
The increasing move towards open access full-text scientific literature enhances our ability to u... more The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from 'reading the literature'. The utility of text-mining for well-studied species is obvious though the utility for less studied species, or those with no prior track-record at all, is not clear. Here we present a concept for how advanced text-mining can be used to create information-rich networks even for less well studied species and apply it to generate an open-access gene-gene association network resource for Synechocystis sp. PCC 6803, a representative model organism for cyanobacteria and first case-study for the methodology. By merging the text-mining network with networks generated from species-specific experimental data, network integration was used to enhance the accuracy of predicting novel interactions that are biologically relevant. A rule-based algor...
Summary Pyridine nucleotide transhydrogenase (PntAB) is an integral membrane protein complex part... more Summary Pyridine nucleotide transhydrogenase (PntAB) is an integral membrane protein complex participating in the regulation of NAD(P)+:NAD(P)H redox homeostasis in various prokaryotic and eukaryotic organisms. In the present study we addressed the function and biological role of PntAB in oxygenic photosynthetic cyanobacteria capable of both autotrophic and heterotrophic growth, with support from structural three‐dimensional (3D)‐modeling. The pntA gene encoding the α subunit of heteromultimeric PntAB in Synechocystis sp. PCC 6803 was inactivated, followed by phenotypic and biophysical characterization of the ΔpntA mutant under autotrophic and mixotrophic conditions. Disruption of pntA resulted in phenotypic growth defects observed under low light intensities in the presence of glucose, whereas under autotrophic conditions the mutant did not differ from the wild‐type strain. Biophysical characterization and protein‐level analysis of the ΔpntA mutant revealed that the phenotypic defe...
We present an application of EVEX, a literature-scale event extraction resource, in the concrete ... more We present an application of EVEX, a literature-scale event extraction resource, in the concrete biological use case of NADP(H) metabolism regulation in Escherichia coli. We make extensive use of the EVEX event generalization based on gene family definitions in Ensembl Genomes, to extract cross-species candidate regulators. We manually evaluate the resulting network so as to only preserve correct events and facilitate its integration with microarray-based co-expression data. When analysing the combined network obtained from text mining and co-expression, we identify 41 candidate genes involved in triangular patterns involving both subnetworks. Several of these candidates are of particular interest, and we discuss their biological relevance further. This study is the first to present a real-world evaluation of the EVEX resource in particular and literature-scale application of the systems emerging from the BioNLP Shared Task series in general. We summarize the lessons learned from th...
Proteomes of an oxygenic photosynthetic cyanobacterium, Synechocystis sp. PCC 6803, were analyzed... more Proteomes of an oxygenic photosynthetic cyanobacterium, Synechocystis sp. PCC 6803, were analyzed under photoautotrophic (low and high CO2, assigned as ATLC and ATHC), photomixotrophic (MT), and light-activated heterotrophic (LAH) conditions. Allocation of proteome mass fraction to seven sub-proteomes and differential expression of individual proteins were analyzed, paying particular attention to photosynthesis and carbon metabolism–centered sub-proteomes affected by the quality and quantity of the carbon source and light regime upon growth. A distinct common feature of the ATHC, MT, and LAH cultures was low abundance of inducible carbon-concentrating mechanisms and photorespiration-related enzymes, independent of the inorganic or organic carbon source. On the other hand, these cells accumulated a respiratory NAD(P)H dehydrogenase I (NDH-11) complex in the thylakoid membrane (TM). Additionally, in glucose-supplemented cultures, a distinct NDH-2 protein, NdbA, accumulated in the TM, ...
The increasing move towards open access full-text scientific literature enhances our ability to u... more The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from 'reading the literature'. The utility of text-mining for well-studied species is obvious though the utility for less studied species, or those with no prior track-record at all, is not clear. Here we present a concept for how advanced text-mining can be used to create information-rich networks even for less well studied species and apply it to generate an open-access gene-gene association network resource for Synechocystis sp. PCC 6803, a representative model organism for cyanobacteria and first case-study for the methodology. By merging the text-mining network with networks generated from species-specific experimental data, network integration was used to enhance the accuracy of predicting novel interactions that are biologically relevant. A rule-based algor...
Summary Pyridine nucleotide transhydrogenase (PntAB) is an integral membrane protein complex part... more Summary Pyridine nucleotide transhydrogenase (PntAB) is an integral membrane protein complex participating in the regulation of NAD(P)+:NAD(P)H redox homeostasis in various prokaryotic and eukaryotic organisms. In the present study we addressed the function and biological role of PntAB in oxygenic photosynthetic cyanobacteria capable of both autotrophic and heterotrophic growth, with support from structural three‐dimensional (3D)‐modeling. The pntA gene encoding the α subunit of heteromultimeric PntAB in Synechocystis sp. PCC 6803 was inactivated, followed by phenotypic and biophysical characterization of the ΔpntA mutant under autotrophic and mixotrophic conditions. Disruption of pntA resulted in phenotypic growth defects observed under low light intensities in the presence of glucose, whereas under autotrophic conditions the mutant did not differ from the wild‐type strain. Biophysical characterization and protein‐level analysis of the ΔpntA mutant revealed that the phenotypic defe...
We present an application of EVEX, a literature-scale event extraction resource, in the concrete ... more We present an application of EVEX, a literature-scale event extraction resource, in the concrete biological use case of NADP(H) metabolism regulation in Escherichia coli. We make extensive use of the EVEX event generalization based on gene family definitions in Ensembl Genomes, to extract cross-species candidate regulators. We manually evaluate the resulting network so as to only preserve correct events and facilitate its integration with microarray-based co-expression data. When analysing the combined network obtained from text mining and co-expression, we identify 41 candidate genes involved in triangular patterns involving both subnetworks. Several of these candidates are of particular interest, and we discuss their biological relevance further. This study is the first to present a real-world evaluation of the EVEX resource in particular and literature-scale application of the systems emerging from the BioNLP Shared Task series in general. We summarize the lessons learned from th...
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Papers by Sanna Kreula