Detailed information    

experimental Experimentally validated

Overview

Name   comM   Type   Regulator
Locus tag   SPD_RS09290 Genome accession   NC_008533
Coordinates   1737234..1737854 (-) Length   206 a.a.
NCBI ID   WP_000839908.1    Uniprot ID   A0A0B7M636
Organism   Streptococcus pneumoniae D39     
Function   fratricide immunity   
Competence regulation

Function

The comM gene encodes a protein that provides cellular immunity towards lytic enzymes, such as the murein hydrolase CbpD, which is involved in fratricide during competence. ComM protects competent cells from the lytic enzymes produced during the competence state, allowing them to survive and undergo natural transformation.


Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
Genomic island 1726515..1748922 1737234..1737854 within 0


Gene organization within MGE regions


Location: 1726515..1748922
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SPD_RS09220 (SPD_1733) - 1726515..1726712 (-) 198 WP_000890144.1 hypothetical protein -
  SPD_RS09225 (SPD_1734) - 1726716..1727510 (-) 795 WP_001101210.1 hypothetical protein -
  SPD_RS09230 (SPD_1735) - 1727918..1728343 (-) 426 WP_000204065.1 hypothetical protein -
  SPD_RS09235 (SPD_1736) - 1728472..1728831 (-) 360 WP_000749822.1 ImmA/IrrE family metallo-endopeptidase -
  SPD_RS09240 - 1728877..1729083 (-) 207 WP_000366091.1 hypothetical protein -
  SPD_RS09245 - 1729070..1729243 (-) 174 WP_000289349.1 helix-turn-helix domain-containing protein -
  SPD_RS09250 (SPD_1737) lytA 1729602..1730558 (-) 957 WP_000405235.1 N-acetylmuramoyl-L-alanine amidase LytA Auxiliary factor
  SPD_RS09255 (SPD_1738) - 1730934..1732304 (-) 1371 WP_001036271.1 MATE family efflux transporter -
  SPD_RS09265 (SPD_1739) recA 1732611..1733777 (-) 1167 WP_001085462.1 recombinase RecA Machinery gene
  SPD_RS09270 (SPD_1740) cinA 1733832..1735088 (-) 1257 WP_000642701.1 competence/damage-inducible protein A Machinery gene
  SPD_RS09275 (SPD_1741) brpA 1735173..1736189 (-) 1017 WP_000239282.1 biofilm formation/cell division transcriptional regulator BrpA -
  SPD_RS09280 (SPD_1742) - 1736197..1736715 (-) 519 WP_000455537.1 GNAT family N-acetyltransferase -
  SPD_RS09285 (SPD_1743) tsaE 1736705..1737148 (-) 444 WP_000288232.1 tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex ATPase subunit type 1 TsaE -
  SPD_RS09290 (SPD_1744) comM 1737234..1737854 (-) 621 WP_000839908.1 hypothetical protein Regulator
  SPD_RS09300 (SPD_1745) - 1738237..1739100 (-) 864 WP_001093641.1 helix-turn-helix domain-containing protein -
  SPD_RS11945 (SPD_1746) - 1739292..1739462 (+) 171 WP_001227862.1 PhrA family quorum-sensing system peptide -
  SPD_RS09310 (SPD_1747) pneA1 1739565..1739789 (+) 225 WP_000181087.1 two-peptide bacteriocin subunit PneA1 -
  SPD_RS09315 (SPD_1748) pneA2 1739796..1739984 (+) 189 WP_000786759.1 two-peptide bacteriocin subunit PneA2 -
  SPD_RS09320 (SPD_1749) - 1740100..1743090 (+) 2991 WP_000875575.1 type 2 lanthipeptide synthetase LanM family protein -
  SPD_RS09325 (SPD_1750) - 1743440..1744144 (+) 705 WP_001033170.1 flavodoxin family protein -
  SPD_RS09330 (SPD_1751) - 1744125..1745054 (+) 930 WP_000912955.1 M50 family metallopeptidase -
  SPD_RS09335 (SPD_1752) - 1745051..1747159 (+) 2109 WP_000701298.1 peptidase domain-containing ABC transporter -
  SPD_RS09340 (SPD_1753) - 1747183..1748922 (+) 1740 WP_000699969.1 S8 family peptidase -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  comM cbpD negative effect
  cbpD lytA positive effect
  cbpD lytC positive effect
  comE comM positive effect
  comE comW positive effect
  comW comX/comX1 positive effect
  comW comX/comX2 positive effect
  mecA comW negative effect
  clpC comW negative effect
  clpP comW negative effect
  comE comA positive effect
  comA comC/comC1 positive effect
  comE comB positive effect
  comB comC/comC1 positive effect
  comE comE positive effect
  comE comX/comX1 positive effect
  comE comD/comD1 positive effect
  comE comX/comX2 positive effect
  comE comC/comC1 positive effect
  comD/comD1 comE positive effect
  stkP comE positive effect
  ccpA comE positive effect
  comX/comX1 late competence genes positive effect
  clpE comX/comX1 negative effect
  clpP comX/comX1 negative effect
  comC/comC1 comD/comD1 positive effect
  ccpA comD/comD1 positive effect
  comX/comX2 late competence genes positive effect
  clpE comX/comX2 negative effect
  clpP comX/comX2 negative effect
  ccpA comC/comC1 positive effect
  htrA comC/comC1 negative effect
  ciaR comC/comC1 negative effect
  ciaH comC/comC1 negative effect
  comX/comX2 late competence genes positive effect
  comX/comX1 late competence genes positive effect
  htrA comEA/celA/cilE negative effect
  htrA comEC/celB negative effect
  ciaR htrA positive effect
  ciaH htrA positive effect

Sequence

Protein


Download         Length: 206 a.a.        Molecular weight: 23552.72 Da        Isoelectric Point: 10.1254

>NTDB_id=212 SPD_RS09290 WP_000839908.1 1737234..1737854(-) (comM) [Streptococcus pneumoniae D39]
MKSMRILFLLALIQISLSSCFLWKECILSFKQSTAFFIGSMVFVSGICAGVNYLYTRKQEVHSVLASKKSVKLFYSMLLL
INLLGAVLVLSDNLFIKNTLQQELVDFLLPSFFFLFGLDLLIFLPLKKYVRDFLAMLDRKKTVLVTILATLLFLRNPMTI
VSLLIYIGLGLFFAAYLVPNSVKKEVSFYGHIFRDLVLVIVTLIFF

Nucleotide


Download         Length: 621 bp        

>NTDB_id=212 SPD_RS09290 WP_000839908.1 1737234..1737854(-) (comM) [Streptococcus pneumoniae D39]
ATGAAATCAATGAGAATCTTATTTTTGTTAGCTTTAATTCAAATCAGTTTGAGTAGCTGTTTCCTATGGAAGGAATGCAT
CTTGTCCTTTAAACAAAGTACAGCTTTTTTCATCGGAAGCATGGTTTTCGTTTCAGGAATCTGTGCTGGAGTAAATTATC
TTTATACCCGTAAGCAAGAAGTCCATAGTGTCCTAGCCAGTAAGAAGTCGGTGAAGCTTTTTTACAGTATGTTACTCTTA
ATTAATTTGTTAGGAGCTGTTCTTGTTTTGTCAGATAACTTGTTCATCAAAAATACGCTGCAGCAAGAATTAGTTGACTT
TTTATTGCCATCCTTCTTTTTCCTATTTGGGCTAGATTTGCTGATTTTTTTACCCTTGAAAAAATACGTGCGCGATTTTC
TTGCTATGCTGGACAGAAAAAAGACAGTGTTGGTGACTATTTTAGCAACACTTCTTTTCTTAAGAAATCCAATGACCATT
GTCTCACTTCTGATTTATATTGGACTGGGCTTGTTTTTTGCAGCCTATCTTGTCCCAAATTCGGTTAAGAAGGAAGTTTC
CTTTTATGGTCATATTTTCCGAGATCTTGTATTGGTCATTGTTACGCTCATTTTCTTTTAG

Domains


No domain identified.



Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB A0A0B7M636

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  comM Streptococcus pneumoniae R6

100

100

1
  comM Streptococcus pneumoniae TIGR4

100

100

1
  comM Streptococcus mitis SK321

39.024

98.086

0.383
  comM Streptococcus mitis NCTC 12261

39.024

97.619

0.381

Multiple sequence alignment    



References

[1] Vikrant Minhas et al. (2023) Competence remodels the pneumococcal cell wall exposing key surface virulence factors that mediate increased host adherence. PLoS Biology 21(1):e3001990. [PMID: 36716340]
[2] Daniel Straume et al. (2017) Overexpression of the fratricide immunity protein ComM leads to growth inhibition and morphological abnormalities in Streptococcus pneumoniae. Microbiology (Reading, England) 163(1):9-21. [PMID: 27902435]
[3] Leiv Sigve Håvarstein et al. (2006) New insights into the pneumococcal fratricide: relationship to clumping and identification of a novel immunity factor. Molecular Microbiology 59(4):1297-307. [PMID: 16430701]
[4] Scott N Peterson et al. (2004) Identification of competence pheromone responsive genes in Streptococcus pneumoniae by use of DNA microarrays. Molecular Microbiology 51(4):1051-70. [PMID: 14763980]