Three tandem promoters, together with IHF, regulate growth phase dependent expression of the Escherichia coli kps capsule gene cluster

Jia, Jia; King, Jane E.; Goldrick, Marie; Aldawood, Esraa; Roberts, Ian S.

doi:10.1038/s41598-017-17891-0

Cited by 12 publications

(15 citation statements)

References 53 publications

(61 reference statements)

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“…This relationship matches empirical data at the genome wide level, except for genes with high transcription rates [54]. Additionally, we further derived a relationship (Section 'CV 2 and Skewness of single-cell protein expression of a tandem promoter's model' in the S1 Appendix) between MP and the skewness, SP, of the single-cell distribution of protein numbers:…”

Section: Analytical Solution Of the Moments Of The Single-cell Protein Numberssupporting

confidence: 63%

Analytical kinetic model of native tandem promoters in E. coli

Chauhan

Bahrudeen

Palma

et al. 2021

Preprint

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Closely spaced promoters in tandem formation are abundant in bacteria. We investigated the evolutionary conservation, biological functions, and the RNA and single-cell protein expression of genes regulated by tandem promoters in E. coli. We also studied the sequence (distance between transcription start sites ‘dTSS’, pause sequences, and distances from oriC) and potential influence of the input transcription factors of these promoters. From this, we propose an analytical model of gene expression based on measured expression dynamics, where RNAP-promoter occupancy times and dTSS are the key regulators of transcription interference due to TSS occlusion by RNAP at one of the promoters (when dTSS ≤ 35 bp) and RNAP occupancy of the downstream promoter (when dTSS > 35 bp). Occlusion and downstream promoter occupancy are modeled as linear functions of occupancy time, while the influence of dTSS is implemented by a continuous step function, fit to in vivo data on mean single-cell protein numbers of 30 natural genes controlled by tandem promoters. The best-fitting step is at 35 bp, matching the length of DNA occupied by RNAP in the open complex formation. This model accurately predicts the squared coefficient of variation and skewness of the natural single-cell protein numbers as a function of dTSS. Additional predictions suggest that promoters in tandem formation can cover a wide range of transcription dynamics within realistic intervals of parameter values. By accurately capturing the dynamics of these promoters, this model can be helpful to predict the dynamics of new promoters and contribute to the expansion of the repertoire of expression dynamics available to synthetic genetic constructs.Author SummaryTandem promoters are common in nature, but investigations on their dynamics have so far largely relied on synthetic constructs. Thus, their regulation and potentially unique dynamics remain unexplored. We first performed a comprehensive exploration of the conservation of genes regulated by these promoters in E. coli and the properties of their input transcription factors. We then measured protein and RNA levels expressed by 30 Escherichia coli tandem promoters, to establish an analytical model of the expression dynamics of genes controlled by such promoters. We show that start site occlusion and downstream RNAP occupancy can be realistically captured by a model with RNAP binding affinity, the time length of open complex formation, and the nucleotide distance between transcription start sites. This study contributes to a better understanding of the unique dynamics tandem promoters can bring to the dynamics of gene networks and will assist in their use in synthetic genetic circuits.

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Section: Analytical Solution Of the Moments Of The Single-cell Protein Numberssupporting

confidence: 63%

Analytical kinetic model of native tandem promoters in E. coli

Chauhan

Bahrudeen

Palma

et al. 2021

Preprint

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“…Moreover, the simultaneous activation of neighbouring promoters could also establish a cooperative action to favour derepression through its transcriptional activity. This could happen by overcoming not only intrinsic pause and arrest sites but also roadblocks caused by DNA binding proteins [49,50], or through the supercoiling that results from the activation of a promoter that could modulate a nearby promoter [51,52] .…”

Section: Discussionmentioning

confidence: 99%

The S. Typhi leuO gene contains multiple functional promoters

Fernández‐Mora

Sánchez‐Popoca

Altamirano-Cruz

et al. 2021

Journal of Medical Microbiology

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The S. Typhi leuO gene, which codes for the LysR-type transcriptional regulator LeuO, contains five forward promoters named P3, P1, P2, P5 and P4, and two reverse promoters, P6 and P7. The activity of the forward promoters was revealed by primer extension using gene reporter fusions in an S. Typhi hns lrp mutant strain. Likewise, the activity of the reverse promoters was revealed in an hns background. Derepression of the transcription of the chromosomal gene was confirmed by RT-PCR in the hns lrp mutant. The leuOP1 transcriptional reporter fusion, which contained only the major P1 promoter, had a lower expression in a relA spoT mutant strain, indicating that the steady-state levels of the (p)ppGpp alarmone positively regulate it. In contrast, the leuOP3, leuOP5P4, leuOP6 and leuOP7 transcriptional fusions were derepressed in the relA spoT background, indicating that the alarmone has a negative effect on their expression. Thus, the search for genetic regulators and environmental cues that would differentially derepress leuO gene expression by antagonizing the action of the H-NS and Lrp nucleoid-associated proteins, or that would fine-tune the expression of the various promoters, will further our understanding of the significance that multiple promoters have in the control of LeuO expression.

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“…This chain of tropical islands is highly favorable to honey bees because the year-round abundance of nectar and pollen resources 1 that facilitates a high density of feral colonies, and as a result there is a significant concentration of commercial queen producers in the state 2 . Hawai‘i is also one of the last locations on earth where honey bees were devoid of the devastating parasite Varroa destructor that has ravaged feral- and managed honey bee populations globally (with notable exceptions like Australia 3 ). The parasite shifted hosts from Apis cerana to A. mellifera in the 1950s on two separate occasions in Russia and in Japan 4 .…”

Section: Introductionmentioning

confidence: 99%

Introduction of Varroa destructor has not altered honey bee queen mating success in the Hawaiian archipelago

Rusert

Pettis

2021

Sci Rep

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Beekeepers struggle to minimize the mortality of their colonies as a consequence of the parasitic mite Varroa destructor in order to maintain a sustainable managed pollinator population. However, little is known about how varroa mites might diminish local populations of honey bee males (drones) that might affect the mating success of queens. As one of the world’s last localities invaded by varroa mites, the Hawaiian Islands offer a unique opportunity to examine this question by comparing queens mated on mite-infested and mite-free islands. We raised queen bees on four Hawaiian Islands (Kaua‘i, O‘ahu, Maui, and Hawai‘i) and subsequently collected their offspring to determine queen mating frequency and insemination success. No significant difference for mating success was found between the islands with and without varroa mites, and relatively high levels of polyandry was detected overall. We also found a significant association between the number of sperm stored in the queens’ spermathecae and the number of managed colonies within the localities of the queens mated. Our findings suggest that varroa mites, as they currently occur in Hawai‘i, may not significantly reduce mating success of honey bee queens, which provides insight for both the reproductive biology of honey bees as well as the apiculture industry in Hawai‘i.

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Three tandem promoters, together with IHF, regulate growth phase dependent expression of the Escherichia coli kps capsule gene cluster

Cited by 12 publications

References 53 publications

Analytical kinetic model of native tandem promoters in E. coli

Analytical kinetic model of native tandem promoters in E. coli

The S. Typhi leuO gene contains multiple functional promoters

Introduction of Varroa destructor has not altered honey bee queen mating success in the Hawaiian archipelago

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