ArticleNucleic acids research2006
Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 61 citations in OpenAlex.
- Proteome trait regulation of marine Synechococcus elemental stoichiometry under global change.The ISME journal · 2024Article
- Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters.The ISME journal · 2021Article
- Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system.PloS one · 2020Article
- Proteomic Response to Rising Temperature in the Marine CyanobacteriumFrontiers in microbiology · 2019Article
- Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean.Frontiers in microbiology · 2018Article
- Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803.Nucleic acids research · 2017Article
- Transcriptome dynamics of a broad host-range cyanophage and its hosts.The ISME journal · 2016Article
- Effects of low temperature on tropical and temperate isolates of marine Synechococcus.The ISME journal · 2016Article
- Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses.Scientific reports · 2016Article
- Article
- The composition of the global and feature specific cyanobacterial core-genomes.Frontiers in microbiology · 2015Article
- Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey.Briefings in bioinformatics · 2014Review
- Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria.Frontiers in genetics · 2014Review
- Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species.Frontiers in microbiology · 2013Article
- Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in Synechococcus sp. strain WH8102.Applied and environmental microbiology · 2012Article
- Synechococcus sp. Strain PCC 7002 Transcriptome: Acclimation to Temperature, Salinity, Oxidative Stress, and Mixotrophic Growth Conditions.Frontiers in microbiology · 2012Article
- Acclimation of the Global Transcriptome of the Cyanobacterium Synechococcus sp. Strain PCC 7002 to Nutrient Limitations and Different Nitrogen Sources.Frontiers in microbiology · 2012Article
- Article
- Comparative analysis of the Spirulina platensis subcellular proteome in response to low- and high-temperature stresses: uncovering cross-talk of signaling components.Proteome science · 2011Article
- Concerted changes in gene expression and cell physiology of the cyanobacterium Synechocystis sp. strain PCC 6803 during transitions between nitrogen and light-limited growth.Plant physiology · 2011Article
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem, we have predicted a detailed model for the nitrogen assimilation network in cyanobacterium Synechococcus sp. WH 8102 (WH8102) using a computational protocol based on comparative genomics analysis and mining experimental data from related organisms that are relatively well studied. This computational model is in excellent agreement with the microarray gene expression data collected under ammonium-rich versus nitrate-rich growth conditions, suggesting that our computational protocol is capable of predicting biological pathways/networks with high accuracy. We then refined the computational model using the microarray data, and proposed a new model for the nitrogen assimilation network in WH8102. An intriguing discovery from this study is that nitrogen assimilation affects the expression of many genes involved in photosynthesis, suggesting a tight coordination between nitrogen assimilation and photosynthesis processes. Moreover, for some of these genes, this coordination is probably mediated by NtcA through the canonical NtcA promoters in their regulatory regions.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.