Comparative Analysis of Streptococcus pneumoniae Type I Restriction-Modification Loci: Variation in hsdS Gene Target Recognition Domains
Abstract
:1. Importance
2. Introduction
3. Results
3.1. S. pneumoniae hsd Type I Restriction-Modification (R-M) Loci Are Genetically Diverse
3.2. S. pneumoniae hsdS Coding Sequences Were Highly Homologous
4. Discussion
5. Materials and Methods
5.1. Sequence Analysis
5.2. Accession Numbers
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Strain | GenBank No. | Serotype | Body Site Origin | Country of Origin | Reference |
---|---|---|---|---|---|
NT_110_58 | CP007593.1 | NT | Nasopharynx | Switzerland | [26] |
D39 | CP000410.1 | 2 | Blood | ND | [27] |
OXC141 | FQ312027.1 | 3 | Carriage | UK | [28] |
SPN034156 | FQ312045.1 | 3 | ND | Italy | [28] |
SPN994039 | FQ312044.2 | 3 | ND | ND | [28] |
70585 | CP000918.1 | 4 | ND | ND | [29] |
TIGR4 | AE005672.3 | 4 | Blood | Norway | [30] |
670-6B | CP002176.1 | 6B | ND | Spain | [31] |
AP200 | CP002121.1 | 11A | Meningitis | Italy | [32] |
CGSP14 | CP001033.1 | 14 | ND | China | [33] |
TCH8431/19A | CP001993.1 | 19A | ND | USA | [34] |
Hungary19A-6 | CP000936.1 | 19A | ND | Hungary | [35] |
SP61 | CP018137.1 | 19A | Thorax | Germany | [36] |
ST556 | CP003357.2 | 19F | Otitis media | USA | [37] |
Taiwan19F-14 | CP000921.1 | 19F | ND | Taiwan | [28] |
G54 | CP001015.1 | 19F | Respiratory | Italy | [38] |
SWU02 | CP018347.1 | 19F | Sputum | China | [39] |
A026 | CP006844.1 | 19F | ND | China | [40] |
EF3030 | MH319941.1 | 19F | Otitis media | USA | This study |
hsdS Target Recognition Domain | ||||||||
---|---|---|---|---|---|---|---|---|
S. pneumoniae Strain | hsdR | hsdM | creX | 1.1 | 1.2 | 2.1 | 2.2 | 2.3 |
D39 | + | + | + | + | + | + | + | + |
TIGR4 | + | + | + | + | + | + | + | + |
TCH8431/19A | + | + | + | + | + | + | + | + |
Hungary19A-6 | + | + | + | + | + | + | + | + |
SP61 | + | + | + | + | + | + | + | + |
ST556 | + | + | + | + | + | + | + | + |
SPN034156 | + | + | + | + | + | + | + | + |
SPN994039 | + | + | + | + | + | + | + | + |
NT_110_58 | + | + | + | + | + | + | + | + |
670-6B | + | + | + | + | + | + | + | + |
OXC141 | + | + | + | + a | + | + | + | + |
AP200 | + | + | + | + | + a | + | + a | + |
SWU02 | + | + | + | + | + a | + | + | + a |
70585 | + | + | + | + | + | - | + | + |
SP14 | + | + | - | + | + | - | + | + |
Taiwan19F-14 | + | + | - | + | + | - | + | + |
A026 | + | + | - | + | + | + | - | - |
G54 | + | + | - | + b | - | - | + | + a |
EF3030 | + | + | + | + b | - | + | + | + a |
Sum | 19 | 19 | 15 | 19 | 17 | 15 | 18 | 18 |
Included for analysis | 18 | 18 | 15 | 18 | 15 | 15 | 17 | 15 |
Length (amino acid) | 777 | 487 | 265 | 179 | 135 | 186 | 186 | 183 |
Matching residues | 763 | 479 | 261 | 178 | 134 | 185 | 180 | 177 |
Similarity (%) | 98.3 | 98.4 | 98.5 | 99.4 | 99.2 | 99.4 | 96.7 | 96.7 |
S. pneumoniae Strain GenBank | D39 CP000410.1 | AP200 CP002121.1 | 670-6B CP002176.1 | OXC141 FQ312027.1 | TIGR4 AE005672.3 | Hungary19A-6 CP000936.1 | TCH8431/19A CP001993.1 | SP61 CP018137.1 | ST556 CP003357.2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Start | End | Start | End | Start | End | Start | End | Start | End | Start | End | Start | End | Start | End | Start | End | |
Locus | 456,041 | 466,242 | 477,425 | 487,635 | 535,782 | 545,984 | 468,070 | 478,291 | 483,927 | 494,129 | 563,225 | 573,421 | 732,691 | 742,894 | 467,880 | 478,083 | 546,433 | 556,636 |
hsdR | 466,242 | 463,909 | 487,635 | 485,302 | 545,984 | 543,651 | 478,291 | 475,958 | 494,129 | 491,796 | 573,421 | 571,088 | 742,894 | 740,561 | 478,083 | 475,750 | 556,636 | 554,303 |
hsdM | 463,896 | 462,433 | 485,289 | 483,826 | 543,638 | 542,175 | 475,945 | 474,455 | 491,783 | 490,320 | 571,075 | 569,612 | 740,548 | 739,085 | 475,737 | 474,274 | 554,290 | 552,827 |
hsdS | 462,433 | 460,865 | 483,826 | 482,259 | 542,175 | 540,607 | 474,482 | 473,820 | 490,320 | 488,752 | 569,612 | 568,044 | 739,085 | 737,517 | 474,274 | 472,709 | 552,827 | 551,262 |
creX | 460,808 | 460,011 | 482,202 | 481,405 | 540,550 | 539,753 | 472,032 | 472,829 | 487,391 | 488,188 | 566,683 | 567,480 | 736,156 | 736,953 | 471,345 | 472,142 | 549,898 | 550,695 |
hsdS’ | 460,000 | 459,401 | 481,295 | 480,789 | 539,742 | 539,134 | 471,413 | 472,021 | 488,259 | 488,798 | 567,491 | 568,096 | 737,024 | 737,569 | 472,462 | 472,761 | 550,706 | 551,314 |
hsdS’’ | 458,167 | 459,447 | 479,800 | 480,693 | 538,206 | 539,180 | 470,191 | 471,465 | 486,054 | 487,334 | 565,346 | 566,626 | 734,819 | 736,099 | 470,008 | 471,288 | 548,561 | 549,841 |
Hypothetical | 457,860 | 457,997 | 479,245 | 479,382 | 537,224 | 537,343 | 469,883 | 470,020 | 485,746 | 485,883 | 565,038 | 565,175 | 734,366 | 734,217 | 469,322 | 469,441 | 548,253 | 548,390 |
Hypothetical | 457,483 | 457,602 | 478,951 | 479,100 | 537,601 | 537,738 | 469,506 | 469,625 | 485,488 | 485,369 | 564,780 | 564,661 | 734,133 | 734,252 | 469,406 | 469,555 | 547,959 | 548,108 |
glnA | 456,041 | 457,387 | 477,425 | 478,771 | 535,782 | 537,128 | 468,070 | 469,416 | 483,927 | 485,273 | 563,225 | 564,571 | 732,691 | 734,037 | 467,880 | 469,226 | 546,433 | 547,779 |
TRD 1.1 | 461,738 | 462,157 | 483,133 | 483,550 | 541,483 | 541,899 | 473,762 | 474,179 | 489,628 | 490,044 | 568,920 | 569,336 | 738,391 | 738,809 | 473,582 | 473,998 | 552,135 | 552,551 |
TRD 1.2 | 458,173 | 458,577 | 479,559 | 479,967 | 537,915 | 538,319 | 470,197 | 470,601 | 486,060 | 486,464 | 565,352 | 565,756 | 734,825 | 735,229 | 470,014 | 470,418 | 548,567 | 548,971 |
TRD 2.1 | 460,865 | 461,425 | 482,259 | 482,819 | 540,607 | 541,167 | 472,886 | 473,446 | 486,774 | 487,334 | 566,066 | 566,626 | 735,539 | 736,099 | 470,728 | 471,288 | 549,281 | 549,841 |
TRD 2.2 | 458,887 | 459,447 | 480,277 | 480,841 | 539,134 | 539,694 | 471,413 | 471,973 | 488,752 | 489,312 | 568,044 | 568,604 | 737,517 | 738,077 | 472,201 | 472,761 | 550,754 | 551,314 |
TRD 2.3 | 459,399 | 459,952 | 480,795 | 481,346 | 538,605 | 539,180 | 470,911 | 471,459 | 488,247 | 488,798 | 567,539 | 568,090 | 737,012 | 737,563 | 472,715 | 473,266 | 551,268 | 551,819 |
S. pneumoniae Strain | n SPN994039 | SPN034156 | NT_110_58 | SWU02 a | A026 | Taiwan19F-14 | G54 | CGSP14 | 70585 | |||||||||
GenBank | FQ312044.2 | FQ312 | 045.1 | CP007593.1 | CP018347.1 | CP006844.1 | CP000921.1 | CP001015.1 | CP001033.1 | CP000918.1 | ||||||||
start | End | start | End | start | End | start | End | start | End | start | End | start | End | start | End | start | End | |
Locus | 457,352 | 467,573 | 1,574,115 | 1,584,308 | 469,994 | 480,196 | 900,998 | 911,194 | 467,754 | 476,981 | 507,439 | 516,169 | 450,495 | 459,235 | 476,083 | 484,809 | 511,799 | 520,522 |
hsdR | 467,573 | 465,240 | 1,584,308 | 1,581,975 | 480,196 | 477,863 | 911,194 | 908,861 | 476,981 | 474,648 | 516,169 | 513,836 | 459,235 | 456,902 | 484,809 | 482,476 | 520,522 | 518,189 |
hsdM | 465,227 | 463,737 | 1,581,962 | 1,580,499 | 477,850 | 476,387 | 908,848 | 907,385 | 474,635 | 473,172 | 513,823 | 512,360 | 456,889 | 455,426 | 482,463 | 481,000 | 518,176 | 516,713 |
hsdS | 463,764 | 462,174 | 1,580,499 | 1,578,934 | 474,840 | 476,387 | 907,385 | 905,852 | 473,172 | 471,594 | 512,360 | 510,795 | 455,426 | 454,332 | 481,000 | 479,450 | 516,713 | 515,163 |
creX | 460,810 | 461,607 | 1,577,573 | 1,578,370 | 473,476 | 474,273 | 904,481 | 905,278 | 471,537 | 470,740 | Absent | Absent | Absent | Absent | Absent | Absent | Absent | Absent |
hsdS’ | 461,594 | 462226 | 1,578,934 | 1,578,986 | Absent | Absent | 905,337 | 905,895 | Absent | Absent | Absent | Absent | Absent | Absent | Absent | Absent | Absent | Absent |
hsdS’’ | 459,473 | 460,753 | 1,576,236 | 1,577,516 | 472,136 | 473,419 | 903,047 | 904,424 | 469,882 | 470,685 | 509,567 | 510,847 | 452,623 | 453,921 | 478,210 | 479,502 | 513,926 | 514,345 |
Hypothetical | 459,165 | 459,302 | 1,575,928 | 1,576,065 | 471,813 | 471,950 | 902,014 | 902,151 | 469,574 | 469,711 | 508,965 | 509,114 | 451,937 | 452,056 | 477,902 | 478,039 | 513,319 | 513,468 |
Hypothetical | 458,788 | 458,907 | 1,575,551 | 1,575,670 | 471,520 | 471,669 | 901,637 | 901,756 | 469,220 | 469,429 | 508,881 | 509,000 | 452,021 | 452,170 | 477,524 | 477,643 | 513,235 | 513,354 |
glnA | 457,352 | 458,698 | 1,574,115 | 1,575,461 | 469,994 | 471,340 | 900,998 | 901,541 | 467,754 | 469,100 | 507,439 | 508,785 | 450,495 | 451,841 | 476,083 | 477,429 | 511,799 | 513,145 |
TRD 1.1 | 463,041 | 463,461 | 1,579,807 | 1,580,223 | 472,127 | 472,543 | 903,132 | 903,548 | 472,480 | 472,896 | 511,668 | 512,084 | 454,734 | 455,150 | 478,215 | 478,631 | 513,926 | 514,345 |
TRD 1.1’ | Absent | Absent | Absent | Absent | Absent | Absent | Absent | Absent | Absent | Absent | Absent | Absent | 452,629 | 453,045 | Absent | Absent | Absent | Absent |
TRD 1.2 | 459,479 | 459,883 | 1,576,242 | 1,576,646 | 475,707 | 476,111 | 906,528 | 907,110 | 469,888 | 470,291 | 509,573 | 509,977 | Absent | Absent | 480,319 | 480,723 | 516,033 | 516,437 |
TRD 2.1 | 460,193 | 460,753 | 1,576,956 | 1,577,516 | 472,859 | 473,419 | 903,864 | 904,424 | 471,594 | 472,153 | Absent | Absent | Absent | Absent | Absent | Absent | Absent | Absent |
TRD 2.2 | 461,666 | 462,226 | 1,578,429 | 1,578,986 | 474,332 | 474,892 | 905,337 | 905,895 | Absent | Absent | 510,287 | 510,847 | 453,361 | 453,921 | 479,449 | 480,009 | 515,164 | 515,723 |
TRD 2.3 | 462,180 | 462,728 | 1,578,940 | 1,579,491 | 474,846 | 475,397 | 905,852 | 906,401 | Absent | Absent | 510,801 | 511,352 | 453,875 | 454,418 | 478,947 | 479,499 | 514,658 | 515,211 |
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Oliver, M.B.; Swords, W.E. Comparative Analysis of Streptococcus pneumoniae Type I Restriction-Modification Loci: Variation in hsdS Gene Target Recognition Domains. Pathogens 2020, 9, 712. https://doi.org/10.3390/pathogens9090712
Oliver MB, Swords WE. Comparative Analysis of Streptococcus pneumoniae Type I Restriction-Modification Loci: Variation in hsdS Gene Target Recognition Domains. Pathogens. 2020; 9(9):712. https://doi.org/10.3390/pathogens9090712
Chicago/Turabian StyleOliver, Melissa B., and W. Edward Swords. 2020. "Comparative Analysis of Streptococcus pneumoniae Type I Restriction-Modification Loci: Variation in hsdS Gene Target Recognition Domains" Pathogens 9, no. 9: 712. https://doi.org/10.3390/pathogens9090712