Abstract:
:Both intrinsic and extrinsic mechanisms regulating bacterial expression have been elucidated and described, however, such studies have mainly focused on local effects on the two-dimensional structure of the prokaryote genome while long-range as well as spatial interactions influencing gene expression are still only poorly understood. In this paper, we investigate the association between co-expression and distance between genes, using RNA-seq data at multiple growth phases in order to illuminate whether such conserved patterns are an indication of a gene regulatory mechanism relevant for prokaryotic cell proliferation, adaption, and evolution. We observe recurrent sinusoidal patterns in correlation of pairwise expression as function of genomic distance and rule out that these are caused by transcription-induced supercoiling gradients, gene clustering in operons, or association with regulatory transcription factors (TFs). By comparing spatial proximity for pairs of genomic bins with their correlation of pairwise expression, we further observe a high co-expression proportional with the spatial proximity. Based on these observations, we propose that the observed patterns are related to nucleoid structure as a product of transcriptional spilling, where genes actively influence transcription of spatially proximal genes through increases within shared local pools of RNA polymerases (RNAP), and actively spilling transcription onto neighboring genes.
journal_name
Front Microbioljournal_title
Frontiers in microbiologyauthors
Krogh TJ,Franke A,Møller-Jensen J,Kaleta Cdoi
10.3389/fmicb.2020.02002subject
Has Abstractpub_date
2020-09-01 00:00:00pages
2002issn
1664-302Xjournal_volume
11pub_type
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abstract::The High Arctic is dominated by polar desert habitats whose microbial communities are poorly understood. In this study, we used next generation sequencing to describe the α- and β-diversity of microbial communities in polar desert soils from the Kongsfjorden region of Svalbard. Ten phyla dominated the soils and accoun...
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abstract::Microbial communities in the endosphere of Salicaceae plants, poplar (Populus trichocarpa) and willow (Salix sitchensis), have been demonstrated to be important for plant growth promotion, protection from biotic and abiotic stresses, and degradation of toxic compounds. Our study aimed to investigate bio-control activi...
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abstract::Mobile genetic elements, including plasmids, drive the evolution of prokaryotic genomes through the horizontal transfer of genes allowing genetic exchange between bacteria. Moreover, plasmids carry accessory genes, which encode functions that may offer an advantage to the host. Thus, it is expected that in a certain e...
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doi:10.3389/fmicb.2020.01343
更新日期:2020-06-23 00:00:00
abstract::Microorganisms perform countless tasks on Earth and they are expected to be essential for human space exploration. Despite the interest in the responses of bacteria to space conditions, the findings on the effects of microgravity have been contradictory, while the effects of Martian gravity are nearly unknown. We perf...
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pub_type: 杂志文章
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doi:10.3389/fmicb.2016.01094
更新日期:2016-07-14 00:00:00
abstract::The study of inorganic nutrients dynamics in shallow sediments usually focuses on two main pools: porewater (PW) nutrients and exchangeable (EX) ammonium and phosphate. Recently, it has been found that microphytobenthos (MPB) and other microorganisms can accumulate large amounts of nutrients intracellularly (IC), high...
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pub_type: 杂志文章
doi:10.3389/fmicb.2016.00761
更新日期:2016-05-26 00:00:00
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abstract::Chitosan is a natural biopolymer from crab shells that is known for its biocompatibility, biodegradability, and bioactivity. In human medicine, chitosan is used as a stabilizer for active ingredients in tablets, and is popular in slimming diets. Due to its low toxicity, it was the first basic substance approved by the...
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pub_type: 杂志文章,评审
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abstract::A Viable but non-culturable (VBNC) state is a bacterial survival strategy under reverse conditions. It poses a significant challenge for public health and food safety. In this study, the effect of external environmental conditions including acid, nutrition, and salt concentrations on the formation of S. aureus VBNC st...
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更新日期:2020-11-26 00:00:00
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abstract::Babesia species are tick-borne intraerythrocytic protozoa that cause babesiosis in humans worldwide. No vaccine has yet proven effective against Babesia infection. Surface antigens of merozoites are involved in the invasion of erythrocytes by Babesia. Surface antigens may be presented by both babesial sporozoites and ...
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abstract::Haemophilus parasuis is known as a commensal organism discovered in the upper respiratory tract of swine where the pathogenic bacteria survive in various adverse environmental stress. QseC, a histidine protein kinase of the two-component regulatory systems CheY/QseC, is involved in the environmental adaptation in bact...
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abstract::Globally, mosquitoes are known to be competent vectors to various arboviruses that cause serious and debilitating diseases to humans and animals. Conversely, mosquitoes harbor a wide array of insect specific viruses (ISVs) that are generally neglected. Extensive characterization of these ISVs is important in understan...
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