ArticleBMC genomics2013
Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 52 citations in OpenAlex.
- CAP-RNAseq: an integrated pipeline for functional annotation and prioritization of co-expression clusters.Briefings in bioinformatics · 2024Article
- Transcription-replication interactions reveal principles of bacterial genome regulation.Research square · 2023Article
- The noncoding RNA CcnA modulates the master cell cycle regulators CtrA and GcrA in Caulobacter crescentus.PLoS biology · 2022Article
- Article
- Promoter Architecture Differences amongmSystems · 2021Article
- Environmental Conditions Modulate the Transcriptomic Response of BothMicroorganisms · 2021Article
- The Protein Quality Control Network inFrontiers in molecular biosciences · 2021Review
- Untargeted metabolomics links glutathione to bacterial cell cycle progression.Nature metabolism · 2020Article
- The Two Chemotaxis Clusters in Caulobacter crescentus Play Different Roles in Chemotaxis and Biofilm Regulation.Journal of bacteriology · 2019Article
- Periplasmic protein EipA determines envelope stress resistance and virulence in Brucella abortus.Molecular microbiology · 2019Article
- High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization.Nucleic acids research · 2018Article
- Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival.eLife · 2018Article
- A New Essential Cell Division Protein in Caulobacter crescentus.Journal of bacteriology · 2017Article
- Cohesive Properties of themBio · 2017Article
- Dynamic translation regulation in Caulobacter cell cycle control.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Cell cycle progression in Caulobacter requires a nucleoid-associated protein with high AT sequence recognition.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Caulobacter crescentus intrinsic dimorphism provides a prompt bimodal response to copper stress.Nature microbiology · 2016Article
- CauloBrowser: A systems biology resource for Caulobacter crescentus.Nucleic acids research · 2016Article
- Mapping the CgrA regulon of Rhodospirillum centenum reveals a hierarchal network controlling Gram-negative cyst development.BMC genomics · 2015Article
- The bacterial cell cycle regulator GcrA is a σ70 cofactor that drives gene expression from a subset of methylated promoters.Genes & development · 2015Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundThe genetic network involved in the bacterial cell cycle is poorly understood even though it underpins the remarkable ability of bacteria to proliferate. How such network evolves is even less clear. The major aims of this work were to identify and examine the genes and pathways that are differentially expressed during the Caulobacter crescentus cell cycle, and to analyze the evolutionary features of the cell cycle network.
resultsWe used deep RNA sequencing to obtain high coverage RNA-Seq data of five C. crescentus cell cycle stages, each with three biological replicates. We found that 1,586 genes (over a third of the genome) display significant differential expression between stages. This gene list, which contains many genes previously unknown for their cell cycle regulation, includes almost half of the genes involved in primary metabolism, suggesting that these "house-keeping" genes are not constitutively transcribed during the cell cycle, as often assumed. Gene and module co-expression clustering reveal co-regulated pathways and suggest functionally coupled genes. In addition, an evolutionary analysis of the cell cycle network shows a high correlation between co-expression and co-evolution. Most co-expression modules have strong phylogenetic signals, with broadly conserved genes and clade-specific genes predominating different substructures of the cell cycle co-expression network. We also found that conserved genes tend to determine the expression profile of their module.
conclusionWe describe the first phylogenetic and single-nucleotide-resolution transcriptomic analysis of a bacterial cell cycle network. In addition, the study suggests how evolution has shaped this network and provides direct biological network support that selective pressure is not on individual genes but rather on the relationship between genes, which highlights the importance of integrating phylogenetic analysis into biological network studies.
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Registered trials
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.