Discovery of 20 novel ribosomal leader candidates in bacteria and archaea

BMC Microbiology

Table 1 Summary of novel ribosomal leaders

Most likely ligand	Ligand basis	Regulated gene(s)	Lineage(s)	Motif rating
L2	Closest	rplB, rpsS, rplV, rpsC	Alphaproteobacteria	?
L4	Prior	rplC,rplD, rplW, rplB +	Archaeoglobi (Archaea)	?
L13	Prior	rplM, rpsl, + rpsB	Bacteroidia	Y
eL15 *	Only	rpl15e	Euryarchaeota (Archaea)	Y
L17	Only	rplQ	Actino- and Proteobacteria	Y
L20 *	Only	rpsT	Deltaproteobacteria	Y
L31	Only	rpmE	Actinobacteria	Y
L31	Only	rpmE	Coriobacteria	Y
L31	Prior @	rpmE, rpmF	Corynebacteriaceae	Y
L31	Only	rpmE	Firmicutes	Y
L31	Only	rpmE	Gammaproteobacteria	Y
S4	Prior	rpsD, rpoA, rplQ	Bacteroidia	Y
S4	Prior	rpsM, rpsK,rpsD, rpoA, rplQ	Clostridia	Y
S4	Prior	rpsD, rpoA, rplQ	Flavobacteria	Y
S4 *	Prior	rpsM, rpsK,rpsD, rpoA, rplQ	Fusobacteriales	Y
S6:S18	Prior	rpsF, ssbA,rpsR, rpll	Chlorobi	Y
S15	Only	rpsO	Flavobacteria	?
S15 *	Prior	rpsO, + recJ, rps3ae	Halobacteria (Archaea)	Y
S15 *	Prior	rpsO, + recJ, rps3ae	Methanomicrobia (Archaea)	Y
S16	Only	rpsP, rimM	Flavobacteria	Y

“Most-likely ligand”: see text. All proteins are the bacterial version, except eL15 is the eukaryotic/archaeal “L15” protein. Some principles used for ligand predictions are uncertain (see text). Asterisk (*): r-leader is potentially similar to rRNA binding site for the given ligand, supporting its assignment. “Ligand basis”: principle with which the most likely gene was hypothesized. “Only”: there is only one regulated r-gene; “Prior”: there are multiple regulated genes and one encodes a known ligand of another r-leader (at sign (@): based on L31 motifs in the current paper), “Closest”: the immediately downstream gene. “Regulated gene(s)”: genes consistently located in potentially regulated operons are listed in the order they most often appear. Most genes encode ribosomal proteins. Genes encoding the ligand of a previously established r-leader are underlined. Motifs lacking underlined genes bind novel r-protein ligands. Plus sign: apparent operon can often be extended. (Potential additional genes are shown in three cases.) “Lineage”: taxon containing the motif. Archaeal taxa are indicated. “Motif rating”: covariation evidence supporting assignment as RNA. “Y” = likely candidate, “?” = borderline candidate. The reasons for assigning candidates as borderline are given in Additional file 1: Supplementary text

ISSN: 1471-2180