TABLE 4.
Characteristics of the six plasticity regions identified in this study and prevalence of selected specific genomic sequences in a collection of strains with LP, IP, or HP to induce MLF
| Region | Accession no.a | Predicted functionb | Organism | Size (aa)c | Coordinates (aa)d | E value | % of identity | % of coverage | Total % | Prevalence in HP groupe | Mobilityf |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | YP_810287 | FA2-related hypothetical protein | O. oeni PSU-1 | 339 | 1-91, 125-210 | 1E-37, 6E-22 | 73.4 | 52.2 | Phage-related sequences | ||
| YP_810289* | Hypothetical protein | O. oeni PSU-1 | 191 | 39-191 | 2E-80 | 100 | 80.1 | 88.5 | ns | Flanking DR | |
| YP_810290* | Hypothetical protein | O. oeni PSU-1 | 166 | 26-166 | 4E-65 | 90.7 | 84.9 | 87.2 | ns | 50 bp, imperfect | |
| YP_810291 | Cell surface protein | O. oeni PSU-1 | 164 | 1-25 | 2E-05 | 96.0 | 15.2 | ||||
| 2 | YP_809730 | Hypothetical protein | O. oeni PSU-1 | 123 | 1-123 | 7E-54 | 86.1 | 100 | ni | ||
| YP_809731 | Transcriptional regulator | O. oeni PSU-1 | 453 | 1-48, 298-453 | 2E-26, 1E-82 | 100 | 45.0 | ||||
| YP_809743* | Arabinose efflux permease | O. oeni PSU-1 | 387 | 1-40, 249-387 | 4E-13, 1E-62 | 93.8 | 46.3 | 77.7 | ns | ||
| YP_809745* | 3-Oxo-acyl carrier protein reductase | O. oeni PSU-1 | 252 | 1-57 | 7E-25 | 100 | 22.6 | 79.5 | 4.40 | ||
| YP_809747* | Galactoside-O-acetyltransferase | O. oeni PSU-1 | 177 | 1-150 | 2E-80 | 98.6 | 84.7 | 78.2 | |||
| YP_809748* | NADH quinone reductase | O. oeni PSU-1 | 300 | 88-143, 174-300 | 1E-24, 1E-68 | 100 | 61.0 | 85.9 | ns | ||
| YP_809752* | Hypothetical protein | O. oeni PSU-1 | 129 | 101-129 | 8E-08 | 100 | 21.7 | 73.0 | ns | ||
| YP_809753* | Hypothetical protein | O. oeni PSU-1 | 78 | 1-78 | 7E-27 | 80.7 | 100 | 78.0 | |||
| YP_809754* | Phosphoglycerate mutase | O. oeni PSU-1 | 246 | 1-246 | 1E-134 | 98.8 | 100 | 85.9 | ns | ||
| YP_809755 | Hypothetical protein | O. oeni PSU-1 | 66 | 1-66 | 5E-31 | 100 | 100 | ||||
| 3 | YP_811244* | Polysaccharide transporter, PST family | O. oeni PSU-1 | 479 | 1-74, 160-478 | 3E-23, 1E-136 | 75.3 | 81.6 | 58.9 | ns | ni |
| ATCC BAA-1163 | 479 | 1-74, 160-478 | 3E-23, 1E-136 | 75.0 | |||||||
| YP_811245* | Predicted glycosyltransferase | O. oeni PSU-1 | 269 | 226-268 | 2E-11 | 65.0 | 16.0 | 65.4 | ns | ||
| ATCC BAA-1163 | 269 | 226-268 | 2E-11 | 65.0 | |||||||
| YP_811247* | Glycosyltransferase-related enzyme | O. oeni PSU-1 | 312 | 1-59 | 1E-18 | 71.0 | 18.9 | 57.7 | ns | ||
| ATCC BAA-1163 | 312 | 1-59 | 1E-18 | 71.0 | |||||||
| YP_811251* | Predicted glycosyltransferase | O. oeni PSU-1 | 306 | 6-302 | 1E-80 | 54.3 | 97.1 | 65.4 | ns | ||
| ATCC BAA-1163 | 306 | 6-302 | 1E-80 | 54.3 | |||||||
| YP_811248 | Hypothetical protein | O. oeni PSU-1 | 455 | 1-29, 315-448 | 1E-04, 8E-51 | 82.7 | 36.0 | ns | ns | ||
| ATCC BAA-1163 | 455 | 1-29, 315-448 | 1E-04, 8E-51 | 82.6 | |||||||
| YP_811249* | Capsular polysaccharide biosynthesis protein | O. oeni PSU-1 | 181 | 72-179 | 6E-36 | 66.6 | 59.7 | 60.2 | ns | ||
| ATCC BAA-1163 | 181 | 72-179 | 6E-36 | 66.6 | |||||||
| 4 | NP_786654* | Hypothetical protein | L. plantarum | 323 | 1-323 | 1E-165 | 94.0 | 100 | 16.7 | ns | Flanking IS |
| NP_786185* | Hypothetical protein | L. plantarum | 117 | 58-117 | 3E-20 | 83.3 | 51.3 | 14.0 | 3.6 | ||
| YP_809989 | Hypothetical protein | O. oeni PSU-1 | 67 | 1-67 | 6E-17 | 75.7 | 100 | ||||
| YP_809985* | Cadmium transport ATPase | O. oeni PSU-1 | 634 | 1-551 | 0.0 | 84.2 | 86.9 | 21.8 | 4.6 | ||
| YP_809986* | GlpF aquaglyceroporin | O. oeni PSU-1 | 250 | 1-112 | 6E-57 | 92.0 | 44.8 | 20.5 | ns | ||
| NP_786657* | Thioredoxin | L. plantarum | 106 | 9-106 | 3E-50 | 97.9 | 92.5 | 35.9 | ns | ||
| YP_809988* | Hypothetical protein | L. plantarum | 89 | 1-82 | 1E-33 | 90.2 | 92.1 | 29.5 | ns | ||
| YP_809990* | Dps | O. oeni PSU-1 | 184 | 1-184 | 6E-92 | 98.2 | 100 | 16.7 | 4.3 | ||
| YP_809991* | Copper chaperone | O. oeni PSU-1 | 74 | 1-57 | 9E-24 | 96.4 | 100 | 23.0 | 5.0 | ||
| YP_809992* | Fnr-like protein | O. oeni PSU-1 | 221 | 1-221 | 1E-116 | 98.6 | 100 | 33.3 | 5.7 | Flanking IS | |
| 5 | NP_784135 | Acetyltransferase | L. plantarum | 161 | 1-113 | 3E-23 | 47.7 | 70.2 | ni | ||
| NP_786731* | 6-Phospho-beta-glucosidase | L. plantarum | 480 | 1-476 | 0 | 72.6 | 99.2 | 48.7 | ns | ||
| YP_279925* | PTS, beta-glucoside-specific IIABC | S. pyogenes | 620 | 201-602 | 1E-116 | 51.3 | 64.8 | 42.3 | ns | ||
| NP_786735* | Maltose phosphorylase | L. plantarum | 734 | 590-734 | 2E-26 | 50.0 | 19.7 | 36.9 | 5.0 | ||
| 6 | YP_330359* | PTS, fructose-specific, IIC | S. agalactiae | 367 | 1-338 | 1E-119 | 63.0 | 92.1 | 5.1 | ns | ni |
| YP_330360* | PTS, fructose-specific, IIA | S. agalactiae | 149 | 8-149 | 9E-32 | 53.2 | 95.3 | 5.1 | ns | ||
| YP_330361 | PTS, fructose-specific, IIB | S. agalactiae | 103 | 1-87 | 8E-10 | 44.8 | 84.5 |
a
Order as found in O. oeni IOEB Sarco 1491. Asterisks indicate sequences used in the distribution analysis.
b
A statistically significant positive association was found between HP strains and the presence of the sequences with the functions highlighted in bold.
c
aa, amino acids.
d
Amino acid position in BBH.
e
Chi-square value (see Materials and Methods) expressing the preferred distribution of each of the eight tester-specific sequences in the HP group and IP plus LP groups. ns, nonsignificant.
f
Mobility-associated features (phage-related sequences, DRs, or ISs). ni, not identified.