Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens
- Program in Microbiome Dynamics, University of Massachusetts Chan Medical School, United States
- Department of Microbiology, University of Massachusetts Chan Medical School, United States
- Program in Systems Biology, University of Massachusetts Chan Medical School, United States
Figures
Figure 1 with 4 supplements
Novel class IIb microcins are found in numerous Enterobacteriaceae genomes.
(A) Sequence alignments of the newly identified microcin and immunity genes with the gene clusters of E. coli (Ec) CA46 and K. pneumoniae (Kp) RYC492 using Easyfig (Sullivan et al., 2011). …
Figure 1—figure supplement 1
Comparison of class IIb microcin gene clusters from E. coli CA46 and K. pneumoniae RYC492.
BLAST sequence comparison of gene clusters was created using Easyfig (Sullivan et al., 2011). (A) Antimicrobial and immunity genes of each cluster are represented by darker and lighter shades, …
Figure 1—figure supplement 2
Comparison of class IIb microcin gene cluster from newly identified genomes with E. coli CA46 and K. pneumoniae RYC492.
BLAST sequence comparison of gene clusters was created using Easyfig (Sullivan et al., 2011). (A-G) Antimicrobial and immunity genes of each cluster are represented by darker and lighter shades, …
Figure 1—figure supplement 3
Region and domain prediction of antimicrobial (A) and immunity peptides (B) using SMART (Letunic et al., 2021).
Previously known proteins are highlighted in bold.
Figure 1—figure supplement 4
Phylogeny of all microcins from the classes I, IIa, and IIb.
(A) Phylogenetic tree of all known microcin genes using codon-aligned nucleotide sequences with general time reversible model with discrete gamma distribution (GTR+G). The respective signal peptides …
Figure 2
Novel class IIb microcins are effective inhibitors of Enterobacteriaceae and Gram-negative ESKAPE pathogens.
(A) Heatmap summarizing the inhibitory potential of known and novel class IIb microcins against a library of Enterobacteriaceae, Pseudomonadales, and Gram-positive bacteria, including …
Tables
Table 1
Blastp results and closest matches to the known class IIb microcins MccE492, MccG492, MccH47, MccI47, or MccM.
Red color indicates no significant match found.
| Microcin name | Species | Accession no. | Antimicrobial gene name | Antimicrobial closest match | Identical/total length | E-value | Immunity gene name | Immunity closest match | Identical/total length | E-value |
|---|---|---|---|---|---|---|---|---|---|---|
| Bg E492 | Brenneria goodwinii | CP014137 | Bg E492A | Kp E492A (mceA) | 35/106 | 2.00E-14 | Bg E492I | Kp E492I (mceB) | 14/94 | 6.00E-04 |
| Bg X | Brenneria goodwinii | CP014137 | Bg XA | Kp E492A (mceA) | 21/98 | 6.90E-02 | Bg XI | Ec MI (mcmI) | 10/78 | 2.60E+00 |
| Gq W | Gibbsiella quercinecans | CP014136 | Gq WA | Ec I47A (mciA) | 7/103 | 8.10E+00 | Gq WI | Ec MI (mcmI) | 8/74 | 3.30E+02 |
| Ko H47 | Klebsiella oxytoxa | CP033844 | Ko H47A | Ec H47A (mchB) | 32/77 | 1.00E-07 | Ko H47I | Ec H47I (mchI) | 19/69 | 2.00E-14 |
| Ps G492 | Pantoea sp. | CP034363 | Ps G492A | Kp G492A (mceL) | 43/89 | 6.00E-09 | Ps G492I | Kp G492I (mceM) | 37/85 | 2.00E-20 |
| Ro Z | Raoultella ornithinolytica | CP008886 | Ro ZA | Ec MA (mcmA) | 21/64 | 1.00E-03 | Ro ZI | Ec MI (mcmI) | 5/74 | 2.00E+01 |
| Ro H47 | Raoultella ornithinolytica | CP008886 | Ro H47A | Ec H47A (mchB) | 31/79 | 2.00E-07 | Ro H47I | Ec H47I (mchI) | 21/69 | 4.00E-14 |
| Ro I47 | Raoultella ornithinolytica | CP008886 | Ro I47A | Ec I47A (mciA) | 37/79 | 4.00E-26 | Ro I47I | Ec I47I (mciI) | 64/135 | 1.00E-43 |
| Ro X | Raoultella ornithinolytica | CP008886 | Ro XA | Ec MA (mcmA) | 18/99 | 4.40E-01 | Ro XI | Ec MI (mcmI) | 9/61 | 1.00E-02 |
| Sf H47 | Serratia fonticola | CP033055 | Sf H47A | Ec H47A (mchB) | 38/87 | 8.00E-11 | Sf H47I | Ec H47I (mchI) | 48/68 | 4.00E-22 |
| Se G492 | Salmonella enterica | CP030220 | Se G492A | Kp G492A (mceL) | 56/85 | 1.00E-11 | Se G492I | Kp G492I (mceM) | 38/84 | 1.00E-23 |
| Se M | Salmonella enterica | CP030220 | Se MA | Ec MA (mcmA) | 34/90 | 1.00E-17 | Se MI | Ec MI (mcmI) | 38/71 | 6.00E-04 |
Additional files
-
Supplementary file 1
Blastp results and closest matches to the known or novel class IIb microcins.
Red color indicates no significant match found.
- https://cdn.elifesciences.org/articles/102912/elife-102912-supp1-v1.xlsx
-
MDAR checklist
- https://cdn.elifesciences.org/articles/102912/elife-102912-mdarchecklist1-v1.pdf
