Investigating the Relationship between CRISPR-Cas Content and Growth Rate in Bacteria

Liu, Zhiling; Hu, Enze; Niu, Deng-Ke

doi:10.1128/spectrum.03409-22

Cited by 3 publications

(4 citation statements)

References 38 publications

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“…In the PGLS correlation analysis of an empirical dataset (Liu et al, 2023), we found that switching dependent and independent variables could lead to a significant incidence of conflicting results. To investigate this further, we simulated the evolution of two traits (ܺ ଵ and ܺ ଶ ) along a binary tree with 100 terminal nodes, using different models and variances for 16000 iterations.…”

Section: Discussionmentioning

confidence: 99%

“…A dataset including the empirical minimal doubling times, CRISPR spacer numbers, optimal growth temperature, and prophage numbers of 262 bacteria was extracted from the Supplemental Material Table S1 of Liu et al (2023). The phylogenetic tree of these 262 bacteria was retrieved from the Genome Taxonomy Database (GTDB; accessed April 8, 2022) (Parks et al, 2022).…”

Section: Empirical Datasetsmentioning

confidence: 99%

“…Using a dataset comprising a range of traits from 262 bacteria in a recent publication (Liu et al, 2023), we analyzed the correlations of empirical minimal doubling time and optimal growth temperature with genomic characteristics. Thirty-eight pairs of traits were re-examined using Pagel's λ model in the PGLS approach.…”

Section: Switching Dependent and Independent Variables In Pgls Analys...mentioning

confidence: 99%

“…Pagel's λ model was used in these analyses. The dataset containing 262 bacteria was extracted from the Supplemental Material Table S1 of Liu et al (2023), and the phylogenetic tree used in PGLS analysis was retrieved from the Genome Taxonomy Database (Parks et al, 2022). EMDT, empirical_minimal_doubling_times; OPT, mean_optimal_growth_temperature.…”

Section: Switching Dependent and Independent Variables In Pgls Analys...mentioning

confidence: 99%

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Dependent variable selection in phylogenetic generalized least squares regression analysis under Pagel’s lambda model

Chen

Hua

Niu

2023

Preprint

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Phylogenetic generalized least squares (PGLS) regression is one of the most commonly used methods in examining evolutionary correlations between two traits. Unlike the conventional correlation methods like Pearson and Spearman's rank tests, the two analyzed traits are in different positions when correcting the phylogenetic non-independence in PGLS regression. In examining the correlations of CRISPR-Cas and prophage contents with optimal growth temperature and minimal doubling time, we noticed that a remarkable frequency (26.3%) of conflicting results appears after swapping the independent and dependent variables. Then, we generated 12000 simulations of the evolution of two traits (X1andX2) along a binary tree containing 100 terminal nodes with different models and variances. In this simulated dataset, swapping the dependent and independent variables gave conflicting results at a frequency of 17.2%. By conventional correlation analysis of the trait changes along the phylogenetic branches (ΔX1and ΔX2), we established a golden standard for whetherX1andX2correlate in each simulation. With this golden standard, we compared six potential criteria for dependent variable selection, log-likelihood, Akaike information criterion, R2,p-value, Pagel's λ, and the estimated λ in Pagel's λ model. The last two criteria were found to be equivalent in their performance of dependent variable selection and superior to the other four criteria. Because Pagel's λ values, as indicators of phylogenetic signals, are generally calculated at the beginning of phylogenetic comparative studies, for practical convenience, we recommend the trait with a higher λ value to be used as the dependent variable in future PGLS regressions. Logical analysis of cause and effect should be done after establishing a significant correlation by PGLS regression rather than providing an indicator for the choice of the dependent variable.

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Section: Discussionmentioning

confidence: 99%

Section: Empirical Datasetsmentioning

confidence: 99%

Section: Switching Dependent and Independent Variables In Pgls Analys...mentioning

confidence: 99%

Section: Switching Dependent and Independent Variables In Pgls Analys...mentioning

confidence: 99%

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Dependent variable selection in phylogenetic generalized least squares regression analysis under Pagel’s lambda model

Chen

Hua

Niu

2023

Preprint

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A Review: CRISPR Cas System and the Mechanism With an Inhibition of Binding of CRISPR Cas‐9

Hosen,

Nishat,

Soaib

et al. 2024

Nano Select

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CRISPR Cas system is a revolutionary and precise genome editing system that induces bacterial and archaeal adaptive immunity and already has shown several promising applications in the treatment of genetic diseases and detection of nucleic acid targets. It is a complex tool, comprising diverse effector proteins and guide RNA that can be applied to dissociate and modify genes in living organisms along with the in vitro process. The review concentrates on the advances accomplished from some recent years to 2023 for the emergence of predicting actions of Cas protein with the guide RNA (gRNA), playing a key role in genome editing. This review emphasizes the effect of DNA structure and chromosomal protein on Cas 9 binding with a distinct classification of Cas types. The relevance of this review is highlighted by the significance of the rapid development of wide study methods and their potential impacts on the efficiency of the CRISPR Cas system. We have analyzed recent kinds of literature in this work to integrate a deep learning way that contributes over the next time with some important discussion about viral resistance in eukaryotes along with some cancer treatment strategies, and crop improvement by the CRISPR Cas system.

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Trojan Horse virus delivering CRISPR-AsCas12f1 controls plant bacterial wilt caused by Ralstonia solanacearum

Peng,

Xu,

et al. 2024

mBio

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Plant bacterial wilt caused by Ralstonia solanacearum results in huge losses. Accordingly, developing an effective control method for this disease is urgently required. Filamentous phages, which do not lyse host bacteria and exert minimal burden, offer a potential biocontrol solution. A filamentous phage RSCq that infects R. solanacearum was isolated in this study through genome mining. We constructed engineered filamentous phages based on RSCq by employing our proposed approach with wide applicability to non-model phages, enabling the exogenous genes delivery into bacterial cells. CRISPR-AsCas12f1 is a miniature class 2 type V-F CRISPR-Cas system. A CRISPR-AsCas12f1-based gene editing system that targets the key virulence regulator gene hrpB was developed, generating the engineered phage RSCqCRISPR-Cas. Similar to the Greek soldiers in the Trojan Horse, our findings demonstrated that the engineered phage-delivered CRISPR-Cas system could disarm the key “weapon,” hrpB , of R. solanacearum , in medium and plants. Remarkably, pretreatment with RSCqCRISPR-Cas significantly controlled tobacco bacterial wilt, highlighting the potential of engineered filamentous phages as promising biocontrol agents against plant bacterial diseases. IMPORTANCE Bacterial disease, one of the major plant diseases, causes huge food and economic losses. Phage therapy, an environmentally friendly control strategy, has been frequently reported in plant bacterial disease control. However, host specificity, sensitivity to ultraviolet light and certain conditions, and bacterial resistance to phage impede the widespread application of phage therapy in crop production. Filamentous phages, which do not lyse host bacteria and exert minimal burden, offer a potential solution to overcome the limitations of lytic phage biocontrol. This study developed a genetic engineering approach with wide applicability to non-model filamentous phages and proved the application possibility of engineered phage-based gene delivery in plant bacterial disease biocontrol for the first.

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Investigating the Relationship between CRISPR-Cas Content and Growth Rate in Bacteria

Cited by 3 publications

References 38 publications

Dependent variable selection in phylogenetic generalized least squares regression analysis under Pagel’s lambda model

Dependent variable selection in phylogenetic generalized least squares regression analysis under Pagel’s lambda model

A Review: CRISPR Cas System and the Mechanism With an Inhibition of Binding of CRISPR Cas‐9

Trojan Horse virus delivering CRISPR-AsCas12f1 controls plant bacterial wilt caused by Ralstonia solanacearum

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