title: HrrF is the Fur-regulated small RNA in nontypeable Haemophilus influenzae.
abstract: Nontypeable Haemophilus influenzae (NTHi) are Gram-negative commensal bacteria that reside in the nasopharynx. NTHi can also cause multiple upper and lower respiratory tract diseases that include sinusitis, conjunctivitis, bronchitis, and otitis media. In numerous bacterial species the ferric uptake regulator (Fur) acts as a global regulator of iron homeostasis by negatively regulating the expression of iron uptake systems. However in NTHi strain 86-028NP and numerous other bacterial species there are multiple instances where Fur positively affects gene expression. It is known that many instances of positive regulation by Fur occur indirectly through a small RNA intermediate. However, no examples of small RNAs have been described in NTHi. Therefore we used RNA-Seq analysis to analyze the transcriptome of NTHi strain 86-028NPrpsL and an isogenic 86-028NPrpsLΔfur strain to identify Fur-regulated intergenic transcripts. From this analysis we identified HrrF, the first small RNA described in any Haemophilus species. Orthologues of this small RNA exist only among other Pasteurellaceae. Our analysis showed that HrrF is maximally expressed when iron levels are low. Additionally, Fur was shown to bind upstream of the hrrF promoter. RNA-Seq analysis was used to identify targets of HrrF which include genes whose products are involved in molybdate uptake, deoxyribonucleotide synthesis, and amino acid biosynthesis. The stability of HrrF is not dependent on the RNA chaperone Hfq. This study is the first step in an effort to investigate the role small RNAs play in altering gene expression in response to iron limitation in NTHi.
authors.affiliation: The Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America; The Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, United States of America; Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America.
authors.forename: Estevan A
authors.initials: EA
authors.lastname: Santana
authors.affiliation: The Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America; The Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, United States of America.
authors.forename: Alistair
authors.initials: A
authors.lastname: Harrison
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America.
authors.forename: Xinjun
authors.initials: X
authors.lastname: Zhang
authors.affiliation: The Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America; The Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, United States of America.
authors.forename: Beth D
authors.initials: BD
authors.lastname: Baker
authors.affiliation: The Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America; The Biomedical Genomics Core, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Kelly
authors.affiliation: The Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America; The Biomedical Genomics Core, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America.
authors.forename: Peter
authors.initials: P
authors.lastname: White
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America.
authors.forename: Yunlong
authors.initials: Y
authors.lastname: Liu
authors.affiliation: The Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America; The Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, United States of America; Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America.
authors.forename: Robert S
authors.initials: RS
authors.lastname: Munson
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D006192:Haemophilus Infections / Q000382:microbiology*; D006193:Haemophilus influenzae / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D007501:Iron / Q000378:metabolism; D009305:Nasopharynx / Q000382:microbiology; D011401:Promoter Regions, Genetic; D012329:RNA, Bacterial / Q000235:genetics*; D012097:Repressor Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012097:Repressor Proteins; C068477:ferric uptake regulating proteins, bacterial; D007501:Iron