sRNA chaperone Hfq controls bioluminescence and other phenotypes through Qrr1-dependent and -independent mechanisms in Vibrio fischeri

Tepavčević, Jovanka; Yarrington, Kaitlin D; Fung, Brittany L; Lin, Xuhui; Visick, Karen L.

doi:10.1016/j.gene.2021.146048

Cited by 3 publications

(1 citation statement)

References 77 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study, we selected a broad length range sRNAs-seq data from Aliivibrio fischeri OMVs, available in the National Center for Biotechnology Information (NCBI) database, to evaluate and compare the performance of five aligners. A. fischeri is a Gram negative marine bacterium known for its bioluminescent symbiosis with the squid Euprymna scolopes, in which the A. fischeri sRNA SsrA (tmRNA) and the associated chaperone Hfq (a ubiquitous, Sm-like RNA binding protein) play an essential role ( Moriano-Gutierrez et al, 2020 ; Tepavčević et al, 2022 ). The performance of the five mapping tools was evaluated in terms of alignment and assignment rates, percentage of unmapped/multimapped reads, computational time and additionally the number of different biotypes assigned to sRNAs by each aligner on this particular dataset.…”

Section: Introductionmentioning

confidence: 99%

Benchmarking of five NGS mapping tools for the reference alignment of bacterial outer membrane vesicles-associated small RNAs

Banović Đeri,

Nešić,

Vićić

et al. 2024

Front. Microbiol.

View full text Add to dashboard Cite

Advances in small RNAs (sRNAs)-related studies have posed a challenge for NGS-related bioinformatics, especially regarding the correct mapping of sRNAs. Depending on the algorithms and scoring matrices on which they are based, aligners are influenced by the characteristics of the dataset and the reference genome. These influences have been studied mainly in eukaryotes and to some extent in prokaryotes. However, in bacteria, the selection of aligners depending on sRNA-seq data associated with outer membrane vesicles (OMVs) and the features of the corresponding bacterial reference genome has not yet been investigated. We selected five aligners: BBmap, Bowtie2, BWA, Minimap2 and Segemehl, known for their generally good performance, to test them in mapping OMV-associated sRNAs from Aliivibrio fischeri to the bacterial reference genome. Significant differences in the performance of the five aligners were observed, resulting in differential recognition of OMV-associated sRNA biotypes in A. fischeri. Our results suggest that aligner(s) should not be arbitrarily selected for this task, which is often done, as this can be detrimental to the biological interpretation of NGS analysis results. Since each aligner has specific advantages and disadvantages, these need to be considered depending on the characteristics of the input OMV sRNAs dataset and the corresponding bacterial reference genome to improve the detection of existing, biologically important OMV sRNAs. Until we learn more about these dependencies, we recommend using at least two, preferably three, aligners that have good metrics for the given dataset/bacterial reference genome. The overlapping results should be considered trustworthy, yet their differences should not be dismissed lightly, but treated carefully in order not to overlook any biologically important OMV sRNA. This can be achieved by applying the intersect-then-combine approach. For the mapping of OMV-associated sRNAs of A. fischeri to the reference genome organized into two circular chromosomes and one circular plasmid, containing copies of sequences with rRNA- and tRNA-related features and no copies of sequences with protein-encoding features, if the aligners are used with their default parameters, we advise avoiding Segemehl, and recommend using the intersect-then-combine approach with BBmap, BWA and Minimap2 to improve the potential for discovery of biologically important OMV-associated sRNAs.

show abstract

Section: Introductionmentioning

confidence: 99%

Benchmarking of five NGS mapping tools for the reference alignment of bacterial outer membrane vesicles-associated small RNAs

Banović Đeri,

Nešić,

Vićić

et al. 2024

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

CRISPR-Cas System and its Role in Quorum-Sensing Processes of Bacteria and Fungi

Nag

2024

Gene Editing in Plants

View full text Add to dashboard Cite

Vibrio fischeri : a model for host-associated biofilm formation

Fung,

Esin,

Visick

2024

J Bacteriol

View full text Add to dashboard Cite

Multicellular communities of adherent bacteria known as biofilms are often detrimental in the context of a human host, making it important to study their formation and dispersal, especially in animal models. One such model is the symbiosis between the squid Euprymna scolopes and the bacterium Vibrio fischeri . Juvenile squid hatch aposymbiotically and selectively acquire their symbiont from natural seawater containing diverse environmental microbes. Successful pairing is facilitated by ciliary movements that direct bacteria to quiet zones on the surface of the squid’s symbiotic light organ where V. fischeri forms a small aggregate or biofilm. Subsequently, the bacteria disperse from that aggregate to enter the organ, ultimately reaching and colonizing deep crypt spaces. Although transient, aggregate formation is critical for optimal colonization and is tightly controlled. In vitro studies have identified a variety of polysaccharides and proteins that comprise the extracellular matrix. Some of the most well-characterized matrix factors include the symbiosis polysaccharide (SYP), cellulose polysaccharide, and LapV adhesin. In this review, we discuss these components, their regulation, and other less understood V. fischeri biofilm contributors. We also highlight what is currently known about dispersal from these aggregates and host cues that may promote it. Finally, we briefly describe discoveries gleaned from the study of other V. fischeri isolates. By unraveling the complexities involved in V. fischeri ’s control over matrix components, we may begin to understand how the host environment triggers transient biofilm formation and dispersal to promote this unique symbiotic relationship.

show abstract

sRNA chaperone Hfq controls bioluminescence and other phenotypes through Qrr1-dependent and -independent mechanisms in Vibrio fischeri

Cited by 3 publications

References 77 publications

Benchmarking of five NGS mapping tools for the reference alignment of bacterial outer membrane vesicles-associated small RNAs

Benchmarking of five NGS mapping tools for the reference alignment of bacterial outer membrane vesicles-associated small RNAs

CRISPR-Cas System and its Role in Quorum-Sensing Processes of Bacteria and Fungi

Vibrio fischeri : a model for host-associated biofilm formation

Contact Info

Product

Resources

About