Bacterial systems biology articles within Nature Communications

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  • Article
    | Open Access

    Research on the biology and pathogenicity of ‘Candidatus Liberibacter asiaticus’ (CLas), the bacterium that causes citrus Huanglongbing disease, is hampered by our inability to cultivate it in artificial media. Here, Carter et al. use a high-throughput yeast-two-hybrid screen to identify thousands of interactions between CLas proteins, thus providing insights into their potential functions.

    • Erica W. Carter
    • , Orlene Guerra Peraza
    •  & Nian Wang

  • Article
    | Open Access

    Understanding how cells dynamically adapt to their environment is important, but temporal information about cellular behaviour is often limited. Here, Miano et al. apply unsupervised machine learning to a dataset describing the activity of over 1,800 promoters in E. coli, measured every 10 minutes, defining three primary stages of promoter activation in response to heavy metal stress.

    • Arianna Miano
    • , Kevin Rychel
    •  & Jeff Hasty

  • Article
    | Open Access

    Quantifying the contribution of individual molecular components to complex cellular processes is a grand challenge in systems biology. Here, the authors present a general theoretical framework (Functional Decomposition of Metabolism, FDM) to quantify the contribution of every metabolic reaction to metabolic functions, e.g. the synthesis of biomass building blocks.

    • Matteo Mori
    • , Chuankai Cheng
    •  & Terence Hwa

  • Article
    | Open Access

    Bacteria release and respond to autoinducers in a process known as quorum sensing. While classically viewed as a strategy to coordinate cell behaviour, Moreno-Gámez et al. demonstrate using modelling that quorum sensing may also be used to sense the environment as a collective by pooling information at relevant scales and harnessing the wisdom of the crowds.

    • Stefany Moreno-Gámez
    • , Michael E. Hochberg
    •  & G. S. van Doorn

  • Article
    | Open Access

    The interconnected network of cellular metabolism is potentially prone to generating oscillatory behaviour. Here, the authors use single-cell FRET measurements of pyruvate levels to reveal large periodic fluctuations in bacterial glycolysis.

    • Shuangyu Bi
    • , Manika Kargeti
    •  & Victor Sourjik

  • Article
    | Open Access

    Bacteria undergo nutrient fluctuations during repeated feast and famine cycles and need to metabolically adapt to these changes. Using quantitative proteomics, Zhu & Dai show that the stringent response of (p)ppGpp is crucial for the timely adaption of bacterial growth to both amino acid and carbon downshift.

    • Manlu Zhu
    •  & Xiongfeng Dai

  • Article
    | Open Access

    Homeostasis of DNA density is a hallmark of living cells. The authors show via mathematical modelling how two cycles, a titration-based concentration cycle and a nucleotide activation cycle, together drive replication in E. coli at all growth rates.

    • Mareike Berger
    •  & Pieter Rein ten Wolde

  • Article
    | Open Access

    The bacterium E. coli has around 300 transcriptional factors, but the functions of many of them, and the interactions between their respective regulatory networks, are unclear. Here, the authors study genetic interactions among all transcription factor genes in E. coli, revealing condition-dependent interactions and roles for uncharacterized transcription factors.

    • Alla Gagarinova
    • , Ali Hosseinnia
    •  & Mohan Babu

  • Article
    | Open Access

    While phosphorylation is an essential post-translational modification in eukaryotes only recently the phosphoproteome of prokaryotes has been provided. Here, Schastnaya et al. mutate 52 phosphosites on 23 E. coli enzymes and apply metabolomics to provide evidence for the functional relevance of bacterial phosphorylation events.

    • Evgeniya Schastnaya
    • , Zrinka Raguz Nakic
    •  & Uwe Sauer

  • Article
    | Open Access

    Conjugative plasmids mediate the spread and maintenance of diverse traits in microbial communities, but the conditions underlying plasmid persistence are poorly understood. Here, Wang and You present a modeling framework for analysis of gene flow and prediction of plasmid persistence and abundance in complex communities.

    • Teng Wang
    •  & Lingchong You

  • Article
    | Open Access

    The authors set out to identify binding motifs for all 301 transcription factors of a plant pathogenic bacterium, Pseudomonas syringae, using HT-SELEX. They successfully identify binding motifs for 100 transcription factors, infer their binding sites on the genome, and validate the predicted interactions and functions.

    • Ligang Fan
    • , Tingting Wang
    •  & Xin Deng

  • Article
    | Open Access

    Bacterial transcriptomic data have been used to predict antibiotic susceptibility in a species- or antibiotic-specific manner. Here, the authors show that global transcriptional disorder is a common stress response in bacteria with low fitness, and present a general approach that can predict bacterial fitness independently of species or type of stress.

    • Zeyu Zhu
    • , Defne Surujon
    •  & Tim van Opijnen

  • Article
    | Open Access

    Developing cyanobacteria as CO2-neutral cell factories relies on the knowledge of the regulation mechanisms for growth and metabolism. Here, the authors develop an inducible CRISPRi gene repression library in Synechocystis sp. PCC 6803 and screens genes potentially affecting growth and L-lactate tolerance and production.

    • Lun Yao
    • , Kiyan Shabestary
    •  & Elton P. Hudson

  • Article
    | Open Access

    Mechanistic insight into the regulation of transcriptional modules remains scarce. Here, the authors identify statistically independent gene sets by applying independent component analysis to a high-quality E. coli RNA-seq data compendium and find that most gene sets represent the effects of specific transcriptional regulators.

    • Anand V. Sastry
    • , Ye Gao
    •  & Bernhard O. Palsson

  • Article
    | Open Access

    Individual bacteria within isogenic populations can differ in antibiotic tolerance. Here, Libby et al. show that antibiotic tolerance variability can be driven by ‘noisy’ expression of a gene encoding a (p)ppGpp synthetase, which is in turn regulated by multisite phosphorylation of a transcription factor.

    • Elizabeth A. Libby
    • , Shlomi Reuveni
    •  & Jonathan Dworkin

  • Article
    | Open Access

    The virulence of Pseudomonas aeruginosa is regulated by many transcriptional factors (TFs). Here, the authors study the crosstalk between 20 key virulence-related TFs, validate 347 functional target genes, and describe the regulatory relationships of the 20 TFs with their targets in a network that is available as an online platform.

    • Hao Huang
    • , Xiaolong Shao
    •  & Xin Deng

  • Article
    | Open Access

    Environmental stress can affect the outcome of ecological competition. Here, the authors use theory and experiments with a synthetic microbial community to show that a tradeoff between growth rate and competitive ability determines which species prevails when the population faces variable mortality rates.

    • Clare I. Abreu
    • , Jonathan Friedman
    •  & Jeff Gore

  • Article
    | Open Access

    Bacteria grown on two carbon sources either consume both sources simultaneously or consume them sequentially. Here the authors use a metabolic network model of E. coli to show that optimal protein resource allocation and topological features of the network can explain the choice of carbon acquisition.

    • Xin Wang
    • , Kang Xia
    •  & Chao Tang

  • Article
    | Open Access

    Some daughter cells inherit the maternal old pole during bacterial division, but does this correspond to aging? Here, Proenca et al. show that constant patterns of aging and rejuvenation connect distinct growth equilibria within bacterial clonal populations, providing evidence for deterministic age structures.

    • Audrey M. Proenca
    • , Camilla Ulla Rang
    •  & Lin Chao

  • Article
    | Open Access

    How bacteria migrate collectively despite individual phenotypic variation is not understood. Here, the authors show that cells spontaneously sort themselves within moving bands such that variations in individual tumble bias, a determinant of gradient climbing speed, are compensated by the local gradient steepness experienced by individuals.

    • X. Fu
    • , S. Kato
    •  & T. Emonet

  • Article
    | Open Access

    Fast-growing bacteria produce many proteins in excess of what seems optimal for exponential growth. Here, the authors present a mathematical model and experimental evidence supporting that this overexpression serves as a strategic reserve to quickly meet demand upon sudden improvement in growth conditions.

    • Matteo Mori
    • , Severin Schink
    •  & Terence Hwa

  • Article
    | Open Access

    Cooperative behaviour among individuals provides a collective benefit, but is considered costly. Using Pseudomonas aeruginosa as a model system, the authors show that secretion of the siderophore pyoverdine only incurs a fitness cost and favours cheating when its building blocks carbon or nitrogen are growth-limiting.

    • D. Joseph Sexton
    •  & Martin Schuster

  • Article
    | Open Access

    Organisms improve their fitness by adjusting their gene expression to the environment, for example bacteria scale the expression of metabolic enzymes near linearly to their growth rate. Here, the authors show that such linear scaling often maximizes growth rate, but that linear scaling is suboptimal under some conditions.

    • Benjamin D. Towbin
    • , Yael Korem
    •  & Uri Alon

  • Article
    | Open Access

    Hubs tend to be essential for function in protein networks within organisms. Here, the authors show that during infection, it is the proteins with high centrality in theY. pestishost–pathogen interactome that are most important for pathogen fitness during infection, and highlight the importance of pathogen proteins that likely cause significant perturbation of the host interactome.

    • Núria Crua Asensio
    • , Elisabet Muñoz Giner
    •  & Marc Torrent Burgas

  • Article
    | Open Access

    The bacterial cell wall is important for cell shape and stability, but how the activities of the biosynthetic machinery are coordinated are not clear. Here the authors use single-molecule imaging and chemical perturbations to determine factors that affect the localization dynamics of penicillin-binding proteins (PBP)1A and PBP1B.

    • Timothy K. Lee
    • , Kevin Meng
    •  & Kerwyn Casey Huang

  • Article
    | Open Access

    Sigma factors are regulatory proteins that reprogram the bacterial RNA polymerase in response to stress conditions to transcribe certain genes, including those for other sigma factors. Here, Chauhan et al. describe the complete sigma factor regulatory network of the pathogen Mycobacterium tuberculosis.

    • Rinki Chauhan
    • , Janani Ravi
    •  & Maria Laura Gennaro

  • Article
    | Open Access

    Selected reaction monitoring mass spectrometry (SRM-MS) can quantify dynamic changes in protein expression with high sensitivity. Karlsson et al. define optimal detection parameters for 10,412 distinct group A Streptococcus pyogenespeptides, which facilitates proteome-wide SRM-MS studies in this bacterium.

    • Christofer Karlsson
    • , Lars Malmström
    •  & Johan Malmström

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