title: Bacillus subtilis YhaM, a member of a new family of 3'-to-5' exonucleases in gram-positive bacteria.
abstract: A strain of Bacillus subtilis lacking two 3'-to-5' exoribonucleases, polynucleotide phosphorylase (PNPase) and RNase R, was used to purify another 3'-to-5' exoribonuclease, which is encoded by the yhaM gene. YhaM was active in the presence of Mn(2+) (or Co(2+)), was inactive in the presence of Mg(2+), and could also degrade single-stranded DNA. The half-life of bulk mRNA in a mutant lacking PNPase, RNase R, and YhaM was not significantly different from that of the wild type, suggesting the existence of additional activities that can participate in mRNA turnover. Sequence homologues of YhaM were found only in gram-positive organisms. The Staphylococcus aureus homologue, CBF1, which had been characterized as a double-stranded DNA binding protein involved in plasmid replication, was also shown to be an Mn(2+)-dependent exoribonuclease. YhaM protein has a C-terminal "HD domain," found in metal-dependent phosphohydrolases. By structure modeling, it was shown that YhaM also contains an N-terminal "OB-fold," present in many oligosaccharide- and oligonucleotide-binding proteins. The combination of these two domains is unique. Thus, YhaM and 10 related proteins from gram-positive organisms constitute a new exonuclease family.
authors.affiliation: Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine of New York University, New York 10029, USA.
authors.forename: Irina A
authors.initials: IA
authors.lastname: Oussenko
authors.forename: Roberto
authors.initials: R
authors.lastname: Sanchez
authors.forename: David H
authors.initials: DH
authors.lastname: Bechhofer
mesh_terms: D000595:Amino Acid Sequence; D001412:Bacillus subtilis / Q000201:enzymology*; D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000378:metabolism; D005095:Exoribonucleases / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D006094:Gram-Positive Bacteria / Q000201:enzymology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012329:RNA, Bacterial / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004277:DNA, Single-Stranded; D012329:RNA, Bacterial; D012333:RNA, Messenger; D005095:Exoribonucleases