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Firmicutes cis-acting regulatory element (CRE)

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Firmicutes cis-acting regulatory element (CRE) is a CRE recoverded from a RNAseq of Staphylococcus aureus N315 strain ^[1]. The SEED is composed of a 60 nucleotides sequence, corresponding to Teg147 also named sRNA85 or SAOUHSCs103. Its structure is quite conserved among the specie. The final Rfam family is composed of 17 homologous sequences, which all belong the Firmicutes phylum. Frequently among the family, the corresponding sequence was found in the 5' region of the gene labA at a distance of approximately, 20 nucleotides. The protein LabA regulates KaiC which is implicated in the circadian circle regulation among the Cyanobacteria phylum^[2].

S. aureus has a GC content of 33%, which is low among the Firmicutes. Local variation within the genome of this percentage could show a possible DNA acquisition by horizontal transfer. Indeed, Teg147 has a GC content above 40%.^[3]

Summary of the Firmicutes CRE located in the 5' region of genes

ID	Organism strain	Strand	Position in the genome	Distance between the Firmicutes CRE and the gene (in nucleotides)	Gene ID	Gene annotation
CP000253.1	S.aureus subsp. aureus NCTC 8325	antisense	1861487-1861430	241	SAOUHSC_01956	Hypothetical protein^[4]
JMJF01000005.1	S.chromogenes MU 970 SCHR_MU970	antisense	93013- 92953	31	SCHR-07570	Hypothetical protein (authentic frame-shift mutation)^[4]
GG694019.1	Granulicatella adiacens ATCC 49175	sense	83180-83240	20	EEW36808.1	LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown]^[4]
FR889308.1	Clostridium sp. CAG:352	sense	18640-18700	22	BN621_00979	LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown]^[4]
FR889121.1	Eubacterium sp. CAG:251	sense	78580-78640	18	CDC32186.1	LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown]^[4]
FR882256.1	Lachnospiraceae bacterium CAG:215	antisense	14036-13976	19	CDB01384.1	LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown]^[4]
NFIF01000003.1	Blautia sp. An46	sense	27535-27595	42	B5G00_03530	NYN domain-containing protein^[4]
KI535286.1	Eubacterium brachy ATCC 33089	antisense	254894-254834	20	ESE29873.1	NYN domain limkain-b1-type^[4]
JH414699.1	Subdoligranulum sp. 4_3_54A2FAA	antisense	193622-193562	22	EHL72285.1	LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown]^[4]
HF991807.1	Clostridium sp. CAG:678	sense	3955-4015	16	CCY66959.1	LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown]^[4]
JH590863.1	Lachnospiraceae bacterium ACC2	sense	470853-470914	833	EH016010.1	Predicted nuclease of the RNAse H fold, HicB family
JH590863.1	Lachnospiraceae bacterium ACC2	antisense	16453-16394	25	EH016446.1	LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown]^[4]
HF995344.1	Firmicutes bacterium CAG:646	sense	9468-9528	22	CCZ34610.1	LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown]^[4]
FR885222.1	Phascolarctobacterium sp. CAG:207	sense	16452-16513	38	CDB45685.1	LabA Uncharacterized conserved protein, LabA/DUF88 family [Function unknown]^[4]
CP001859.1	CP001859.1	antisense	1843461-1843400	28	Acfer_1667	Hypothetical protein^[4]

References

^ Beaume, Marie; Hernandez, David; Farinelli, Laurent; Deluen, Cécile; Linder, Patrick; Gaspin, Christine; Romby, Pascale; Schrenzel, Jacques; Francois, Patrice (2010-05-20). "Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions". PloS One. 5 (5): e10725. doi:10.1371/journal.pone.0010725. ISSN 1932-6203. PMC 2873960. PMID 20505759.{{cite journal}}: CS1 maint: unflagged free DOI (link)
^ Taniguchi, Yasuhito; Katayama, Mitsunori; Ito, Rie; Takai, Naoki; Kondo, Takao; Oyama, Tokitaka (2007-01-01). "labA: a novel gene required for negative feedback regulation of the cyanobacterial circadian clock protein KaiC". Genes & Development. 21 (1): 60–70. doi:10.1101/gad.1488107. ISSN 0890-9369. PMC 1759901. PMID 17210789.
^ Garcia-Vallvé, S.; Romeu, A.; Palau, J. (2000-11). "Horizontal gene transfer in bacterial and archaeal complete genomes". Genome Research. 10 (11): 1719–1725. doi:10.1101/gr.130000. ISSN 1088-9051. PMC 310969. PMID 11076857. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
^ ^a ^b ^c ^d ^e ^f ^g ^h ⁱ ^j ^k ^l ^m ⁿ Information, National Center for Biotechnology; Pike, U. S. National Library of Medicine 8600 Rockville. "National Center for Biotechnology Information". www.ncbi.nlm.nih.gov. Retrieved 2019-12-12.{{cite web}}: CS1 maint: numeric names: authors list (link)

[1] Beaume, Marie; Hernandez, David; Farinelli, Laurent; Deluen, Cécile; Linder, Patrick; Gaspin, Christine; Romby, Pascale; Schrenzel, Jacques; Francois, Patrice (2010-05-20). "Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions". PloS One. 5 (5): e10725. doi:10.1371/journal.pone.0010725. ISSN 1932-6203. PMC 2873960. PMID 20505759.{{cite journal}}: CS1 maint: unflagged free DOI (link)

[2] Taniguchi, Yasuhito; Katayama, Mitsunori; Ito, Rie; Takai, Naoki; Kondo, Takao; Oyama, Tokitaka (2007-01-01). "labA: a novel gene required for negative feedback regulation of the cyanobacterial circadian clock protein KaiC". Genes & Development. 21 (1): 60–70. doi:10.1101/gad.1488107. ISSN 0890-9369. PMC 1759901. PMID 17210789.

[3] Garcia-Vallvé, S.; Romeu, A.; Palau, J. (2000-11). "Horizontal gene transfer in bacterial and archaeal complete genomes". Genome Research. 10 (11): 1719–1725. doi:10.1101/gr.130000. ISSN 1088-9051. PMC 310969. PMID 11076857. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)

[:0-4] ^ ^a ^b ^c ^d ^e ^f ^g ^h ⁱ ^j ^k ^l ^m ⁿ Information, National Center for Biotechnology; Pike, U. S. National Library of Medicine 8600 Rockville. "National Center for Biotechnology Information". www.ncbi.nlm.nih.gov. Retrieved 2019-12-12.{{cite web}}: CS1 maint: numeric names: authors list (link)

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