MSMEG6009 (MSMEG6009)

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 MSMEG6005 MSMEG6006 MSMEG6008 MSMEG6009 MSMEG6010 MSMEG6011 MSMEG6012
Species: M. smegmatis
Strain: MC2-155
PATRIC Annotation: -
Synonyms:
M. tuberculosis homologs RVBD3557c, RVBD0273c, RVBD3405c, RVBD3208, RVBD3173c, [+ 4 remaining orthologs]
M. abscessus homologs MAB0599, MAB0483c, MAB3313c, MAB1525c, MAB2543c, [+ 12 remaining orthologs]
Gene Start: 6073484
Gene End: 6074101
Vulnerability Index (VI): 0.2090
VI Lower Bound: -0.3170
VI Upper Bound: 0.8600

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 and Protein Sequence help

DNA Sequence

GTACGTCGCGGCGCGGAGCCAAGGCCATAGCGGCCAACCCGCCGAGGGCGGCGATGAAAGGGACACTGCTCACGGGCTACTCCAGCGTCTCGTCATCGGGTGCGCTCCCGTTGTCGAGCAGGCTACCTGTGAGGTGGGGTGAGGTACTGGGTCTCACCTCGCGAGGGTAGTGCGTGCGACGCCGAGACTGCACTGAGGGACACGTCCCGGCGATTTTTTGTCCCTGGATGCAATCTCGGCGCGTGGTGGCATCTCCCGCCCGACGTGACCTAGCAAGTGCTTGGTTGGTATGCTGGGTCAATGGCGCCGGATACGCCCAGCCAGCCGGCTAGCAGACGCGATGAGCTGCTGCAGCTCGCCGCCACCATGTTCGCCGACCGTGGCCTCAAGGCCACGACGGTCCGCGACATCGCCGACTCCGCAGGCATTCTCTCGGGCAGCCTGTACCACCATTTCAAGTCCAAAGAGCAGATGGTCGAAGAGGTCCTGCGGGACTTCCTGGACTGGCTGTTCGGCCGCTACCAGCAGATCCTCGACACCGCGACCAGCCCGCTGGAGAAGCTGACGGGCCTTTTCATGGCGTCGTTCGAGGCCATCGAGCACCGGCATGCGCAGGTGGTCATCTACCAGGACGAGGCCAAGCGGCTCTCGGACCTGCCGCAGTTCGACTTCGTCGAGACGCGCAACAAAGAGCAGCGCAAGATGTGGGTCGACATCTTGCAGGAGGGCGTCGCCGACGGCTCGTTCCGTCCCGACCTCGATGTCGACCTGGTCTACCGGTTCATCCGGGACACCACATGGGTTTCGGTTCGCTGGTACAAACCGGGCGGGCCCCTTTCGGCCGAACAGGTCGGCCAGCAGTACCTCGCCATCGTTCTCGGCGGAATCACGCAGTCACAAGGAGATAAACATGCCTGA

Protein Sequence

MAPDTPSQPASRRDELLQLAATMFADRGLKATTVRDIADSAGILSGSLYHHFKSKEQMVEEVLRDFLDWLFGRYQQILDTATSPLEKLTGLFMASFEAIEHRHAQVVIYQDEAKRLSDLPQFDFVETRNKEQRKMWVDILQEGVADGSFRPDLDVDLVYRFIRDTTWVSVRWYKPGGPLSAEQVGQQYLAIVLGGITQSQGDKHA_
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) 0.2090 0.8520
VI Lower Bound -0.3170 -0.9250
VI Upper Bound 0.8600 3.7710

Specific References

General References