MSMEG5038 (MSMEG5038)

background  +5   0  -5 -10 -15 sgRNA L2FC (+ATc/–ATc) TnSeq Gene Essentiality Predictions (1, 2) Essential Growth Defect Non-Essential Growth Advantage Unknown Operon Legend (3) Operon (1) PMID: 28096490 (2) PMID: 31388080 (3) PMID: 26536359 MSMEG5034 MSMEG5035 MSMEG5036 MSMEG5037 MSMEG5038 MSMEG5039 MSMEG5040 MSMEG5041 MSMEG5042
Species: M. smegmatis
Strain: MC2-155
PATRIC Annotation: -
Synonyms:
M. tuberculosis homologs cyp130, cyp123, cyp126, cyp124, cyp140, [+ 5 remaining orthologs]
M. abscessus homologs MAB1406c, MAB1216c, MAB3961c, MAB4456, MAB0276, [+ 6 remaining orthologs]
Gene Start: 5132901
Gene End: 5134121
Vulnerability Index (VI): 0.0890
VI Lower Bound: -0.3780
VI Upper Bound: 0.7880

Essentiality:

Call Condition Type Source Notes
Non Essential in vitro TnSeq [Akusobi et al. (2022)]
Non Essential in vitro CRISPRi [Bosch & DeJesus et al. (2021)]


DNA Sequence help
TGAGCACCGGGGCACCCTCGCGGACCTTGCCGCCGAACCGGGTGCGCGGCTCCGGCACCGTGCGTGCGGCCGCGTTGACGCAGTCCACGCACTGGTGGCCGACGGCGGCCGTGCGCATGCACTCCGGGCAGATGAAGCGGTGGCAACGCGTGCAGCTGACGTAGGTCGGCCGGTCCGGATGCCGATAACACGTCGGGACCTGCGCAGGCGGTGGCGGCGGGTACGGGGTGCTCACCGCGCCGAGCCTAGTGCGCAACGTGGCATTGACACATCAGTGGCCTGTGTCATACGAATAAGACATGGGAGCTGATTTGTCTCACCCGGCCGTCGCGTTCGAGCTCGCGAACGCCGACACATGGGCCGACCCGTGGGACATGTACACCGCGCTGCGCGACCACGATCCCGTGCACCACGTCGTCCCGCCCGAACGCCCGCACCACGACTACTTCGTGCTGAGCCGCCACGCCGACATCTGGGCCGCCGCGCGCGATCACGAGACGTACTCGTCGGCGCAGGGGCTCACGGTCAACTACGGCGAGCTGGAGCTGATCGGCCTCGCGGACAATCCGCCGTTCGTCATGCAGGACCCGCCCACGCACACCGAGTTCCGCAAGCTCGTGTCGCGCGGGTTCACCCCGCGTCAGGTCGAGGCCGTCGAGCCGCAAGTCCGCGAGTTCGTGGTGGAACGTCTCGAACGGTTGCGCGCCGAAGGCGGCGGCGACATCGTCGCCGAATTGTTCAAGCCGTTGCCGTCGATGGTGGTCGCGCACTACCTGGGCGTGCCCGAGGCCGACCGTGCGCAGTTCGACGGCTGGACCGAGGCCATCGTCGCGGCCAACAGCGAGGCGGGCTCGGCCCTGGGCGCCGGTGACGCGGTGATGTCGATGACGGGTTACTTCGCCGAGCTCATCGAGCGGCGCCGCCGCGAACCGGGCGACGACACCATCTCGCATCTGGTGGCCGCCGGTGCCGACGATGAGGCGGTGGACGTGCTGTCCATCCTCGCGTTCACGTTCACGATGGTCACCGGCGGCAACGACACCACCACCGGAATGCTCGGCGGCGCAGTACAACTGCTGCAGCAGCATCCCGATCAGCGGCGTGTGCTCACCGACGATCCGGATCTGATCCCCGACGCCGTCGACGAGTTCCTGCGGCTCACCTCCCCCGTTCAGGGCCTGGCGCGCACCGCCACACGCGACGTCACGATCGGTGACACCACGATCCCGGCCGGGCGCAAGGTGTTGCTGCTGTACGGCTCGGGCAACCGGGACGAGCGCGAATTCGGCCCGGACGCCGCCCAACTCGACGTCCGCCGCAGGCCACGCAACATCCTGACGTTCAGCCACGGCGCACATTTCTGCCTCGGTGCGGCCGCCGCGCGCATGCAGTCGCGGGTGGCGCTGACCGAACTGCTCACGCGCTGCCCGGATTTCACGGTCGACCTCGACGCCGTGGTGTGGGCGGGCGGCAGCTACGTGCGTCGCCCGCTTTCGGTGCCGTTCCGAGCCGGTGCGTGA
Vulnerability Assesment help
[Full list of passaging experiments]

Experiment: We designed an M. tuberculosis CRISPRi library (RLC12) to target all annotated Mtb genes with single guide RNAs (sgRNAs) of varying predicted knockdown efficiencies. In parallel, we constructed a M. smegmatis CRISPRi library (RLC11) to target all annotated Msmeg genes, similar to the Mtb sgRNA library. RLC12 was transformed into M. tuberculosis H37Rv; RLC11 into M. smegmatis mc2-155. We passaged both CRISPRi libraries for nearly 30 generations in the presence or absence of the CRISPRi-inducer anhydrotetracycline (ATc). At the indicated timepoints, genomic DNA was harvested and the representation of individual sgRNAs was counted using Illumina sequencing. Here, we show sgRNA log2 fold-change values (L2FC) (plus versus minus ATc) over consecutive generations for sgRNAs targeting the gene you selected. sgRNAs are color-coded based on their predicted strength from blue (strength=0; weak) to red (strength=1; strong).

In order to quantify gene vulnerability, data were subsequently analyzed with a hierarchical model at the sgRNA level (two-line model) and gene level (Hill curve). The vulnerability quantification is shown below. [More information]

M. smegmatis Reference Fitness Experiment M. tuberculosis H37Rv Reference Fitness Experiment M. tuberculosis HN878 Reference Fitness Experiment
 
 
M. smegmatis Gene-Level Logistic Regression M. tuberculosis H37Rv Gene-Level Logistic Regression (Most similar ortholog) M. tuberculosis HN878 Gene-Level Logistic Regression (Most similar ortholog)
 
Vulnerability Index (VI) 0.0890 1.0180
VI Lower Bound -0.3780 -0.3520
VI Upper Bound 0.7880 3.3150

Specific References

General References