yydF

secreted antimicrobial peptide, controls [protein|49E70A20CC05DBE485953C0AE34E634EFB33C3B2|LiaR]-[protein|9A1871BD853254EEA8B4E78CA187F9315CBDF43D|LiaS] activity

locus: BSU_40180

pI: 9.57

mw: 5.65 kDa

protein length: 49 aa

gene length: 150 bp

function: conpetition with other bacteria, control of [protein|49E70A20CC05DBE485953C0AE34E634EFB33C3B2|LiaR]-[protein|9A1871BD853254EEA8B4E78CA187F9315CBDF43D|LiaS] activity

product: secreted antimicrobial peptide

essential: no

synonyms

Genomic Context

categories

• [category|SW 2|Metabolism] → [category|SW 2.6|Additional metabolic pathways] → [category|SW 2.6.6|Miscellaneous metabolic pathways] → [category|SW 2.6.6.1|Biosynthesis of antibacterial compounds]
• [category|SW 3|Information processing] → [category|SW 3.4|Regulation of gene expression] → [category|SW 3.4.2|Transcription factors and their control] → [category|SW 3.4.2.2|Control of two-component response regulators] → [category|SW 3.4.2.2.3|Control of response regulators/ other]
• [category|SW 4|Lifestyles] → [category|SW 4.3|Coping with stress] → [category|SW 4.3.15|Biosynthesis of antibacterial compounds]
• [category|SW 6|Groups of genes] → [category|SW 6.12|Secreted proteins]

Gene

Coordinates: 4,127,498 → 4,127,647

The protein

Modification

• modified (epimerization of Val-36 and Ile-44 to the D-forms) by the radical SAM epimerase [protein|25FC87037222084ABE318813959101016FEB49DF|YydG] [Pubmed|28644475,23106164]
• processing to the mature modified peptide (epipeptide) by the membrane protease [protein|E280A5994F4D9D93DA4B698E79C86360DBEE5396|YydH] [pubmed|28644475]

[SW|Localization]

• extracellular (processing requires [protein|E280A5994F4D9D93DA4B698E79C86360DBEE5396|YydH], transport by [protein|1BF1A48CF645249CA9ECBB19C04B059B11D821EF|YydI]-[protein|A4213DE6C9BE29405B0A4C0A969A78EA4C5EB71F|YydJ]) [Pubmed|23106164]

Expression and Regulation

Operons

• genes: [gene|D66B9BFF79ADD8B0F9BFA3892FCF4597264CE9EE|yydF]-[gene|25FC87037222084ABE318813959101016FEB49DF|yydG]-[gene|E280A5994F4D9D93DA4B698E79C86360DBEE5396|yydH]-[gene|1BF1A48CF645249CA9ECBB19C04B059B11D821EF|yydI]-[gene|A4213DE6C9BE29405B0A4C0A969A78EA4C5EB71F|yydJ]
  description: [Pubmed|17921301]

  sigma factors

  • [protein|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA]: sigma factor, [Pubmed|17921301], in [regulon|360F48D576DE950DF79C1A2677B7A35A8D8CC30C|SigA regulon]

  regulatory mechanism

  • [protein|E5110D9C36E8C55AFD1419987B14A53232165F20|AbrB]: repression, [Pubmed|17921301], in [regulon|E5110D9C36E8C55AFD1419987B14A53232165F20|AbrB regulon]
  • [protein|1508770D5BCA5739D13E3ABD11CC5C103C07FF25|Rok]: repression, [Pubmed|15743949], in [regulon|1508770D5BCA5739D13E3ABD11CC5C103C07FF25|Rok regulon]

  regulation

  • activated after transition to stationary phase([protein|E5110D9C36E8C55AFD1419987B14A53232165F20|AbrB]) [Pubmed|17921301]

additional information

• the mRNA is very stable (> 15 min) [pubmed|12884008]
• the [gene|D66B9BFF79ADD8B0F9BFA3892FCF4597264CE9EE|yydF] portion of the mRNA belongs to the most stable mRNAs in B. subtilis [pubmed|17921301]

Biological materials

Mutant

• BKE40180 (Δ[gene|D66B9BFF79ADD8B0F9BFA3892FCF4597264CE9EE|yydF]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE40180 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATATTATCCCTCCTCCTTT, downstream forward: _UP4_TAATTAGAGGGGTACAAAGG
• BKK40180 (Δ[gene|D66B9BFF79ADD8B0F9BFA3892FCF4597264CE9EE|yydF]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK40180 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATATTATCCCTCCTCCTTT, downstream forward: _UP4_TAATTAGAGGGGTACAAAGG

References

Reviews

• 23106164

Original publications

• 12884008,17921301,17921301,21815947,23199363,28644475,32117169