A Flexible Mathematical Model Platform for Studying Branching Networks: Experimentally Validated Using the Model Actinomycete, Streptomyces coelicolor

Nieminen, Leena; Webb, Steven D.; Smith, Margaret C. M.; Hoskisson, Paul A.

doi:10.1371/journal.pone.0054316

Cited by 24 publications

(19 citation statements)

References 43 publications

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“…Helped by the strong increase in computing power in the modern era, new models were developed recently (392,393). In particular, a three-dimensional model was developed that includes parameters such as hyphal growth, branching, fragmentation, cross-wall formation, and collision detection, as well as oxygen diffusion (392).…”

Section: Correlation Between Growth and Antibiotic Productionmentioning

confidence: 99%

Taxonomy, Physiology, and Natural Products of Actinobacteria

Barka

Vatsa

Sanchez

et al. 2016

Microbiol Mol Biol Rev

1,530

1,048

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SUMMARYActinobacteriaare Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. ManyActinobacteriahave a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture.Actinobacteriaplay diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species ofCorynebacterium,Mycobacterium,Nocardia,Propionibacterium, andTropheryma), soil inhabitants (e.g.,MicromonosporaandStreptomycesspecies), plant commensals (e.g.,Frankiaspp.), and gastrointestinal commensals (Bifidobacteriumspp.).Actinobacteriaalso play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.

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Section: Correlation Between Growth and Antibiotic Productionmentioning

confidence: 99%

Taxonomy, Physiology, and Natural Products of Actinobacteria

Barka

Vatsa

Sanchez

et al. 2016

Microbiol Mol Biol Rev

1,530

1,048

View full text Add to dashboard Cite

show abstract

“…The older models largely focused on the influence of environmental factors on morphology, while genetics-based modeling had not been attempted (Kossen, 2000). Two new models of Streptomyces growth have been developed recently, which should lead to new impetus for modeling of Streptomyces growth and production Nieminen, Webb, Smith, & Hoskisson, 2013). Taking advantage of the incredible increase in computing power since the design of previous models, a three-dimensional in silico model was developed that allows visualization of growth of mycelial pellets with distinct morphologies .…”

Section: Outlook: the Correlation Between Morphology And Productionmentioning

confidence: 99%

Morphogenesis of Streptomyces in Submerged Cultures

Dissel

Claessen

Wezel

2014

Advances in Applied Microbiology

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Members of the genus Streptomyces are mycelial bacteria that undergo a complex multicellular life cycle and propagate via sporulation. Streptomycetes are important industrial microorganisms, as they produce a plethora of medically relevant natural products, including the majority of clinically important antibiotics, as well as a wide range of enzymes with industrial application. While development of Streptomyces in surface-grown cultures is well studied, relatively little is known of the parameters that determine morphogenesis in submerged cultures. Here, growth is characterized by the formation of mycelial networks and pellets. From the perspective of industrial fermentations, such mycelial growth is unattractive, as it is associated with slow growth, heterogeneous cultures, and high viscosity. Here, we review the current insights into the genetic and environmental factors that determine mycelial growth and morphology in liquid-grown cultures. The genetic factors include cell-matrix proteins and extracellular polymers, morphoproteins with specific roles in liquid-culture morphogenesis, with the SsgA-like proteins as well-studied examples, and programmed cell death. Environmental factors refer in particular to those dictated by process engineering, such as growth media and reactor set-up. These insights are then integrated to provide perspectives as to how this knowledge can be applied to improve streptomycetes for industrial applications.

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“…The resumption of growth via branching is intriguing and may involve the serine/threonine protein kinase, AfsK. It is known that branching is affected by environmental conditions 33 and that AfsK plays a role in the onset of secondary metabolism and sporulation, both nutrient dependent processes 34–36 . Recently it has been shown that AfsK co-localizes and directly regulates DivIVA in Streptomyces 36,37 .…”

Section: Resultsmentioning

confidence: 99%

Reconciling DNA replication and transcription in a hyphal organism: Spatial dynamics of transcription complexes in live Streptomyces coelicolor A3(2)

Nieminen¹,

Hoskisson²

2018

Preprint

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Reconciling transcription and DNA replication in the growing hyphae of the filamentous bacterium Streptomyces presents several physical constraints on growth due to their apically extending and branching, multigenomic cells and chromosome replication being independent of cell division. Using a GFP translational fusion to the β`-subunit of RNA polymerase (rpoC-egfp), in its native chromosomal location, we observed growing Streptomyces hyphae using time-lapse microscopy throughout the lifecycle and under different growth conditions. The RpoC-eGFP fusion co-localised with DNA around 1.8 μm behind the extending tip, whereas replisomes localise around 4-5 μm behind the tip, indicating that at the growing tip, transcription and chromosome replication are to some degree spatially separated. Dual-labeled RpoC-egfp/DnaN-mCherry strains also indicate that there is limited co-localisation of transcription and chromosome replication at the extending hyphal tip. This likely facilitates the use of the same DNA molecule for active transcription and chromosome replication in growing cells, independent of cell division. This represents a novel, but hitherto unknown mechanism for reconciling two fundamental processes that utilise the same macromolecular template that allows for rapid growth without compromising chromosome replication in filamentous bacteria and may have implications for evolution of filamentous growth in microorganisms, where uncoupling of DNA replication from cell division is required.

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A Flexible Mathematical Model Platform for Studying Branching Networks: Experimentally Validated Using the Model Actinomycete, Streptomyces coelicolor

Cited by 24 publications

References 43 publications

Taxonomy, Physiology, and Natural Products of Actinobacteria

Taxonomy, Physiology, and Natural Products of Actinobacteria

Morphogenesis of Streptomyces in Submerged Cultures

Reconciling DNA replication and transcription in a hyphal organism: Spatial dynamics of transcription complexes in live Streptomyces coelicolor A3(2)

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