title: Small stress response proteins in Escherichia coli: proteins missed by classical proteomic studies.
abstract: Proteins of 50 or fewer amino acids are poorly characterized in all organisms. The corresponding genes are challenging to reliably annotate, and it is difficult to purify and characterize the small protein products. Due to these technical limitations, little is known about the abundance of small proteins, not to mention their biological functions. To begin to characterize these small proteins in Escherichia coli, we assayed their accumulation under a variety of growth conditions and after exposure to stress. We found that many small proteins accumulate under specific growth conditions or are stress induced. For some genes, the observed changes in protein levels were consistent with known transcriptional regulation, such as ArcA activation of the operons encoding yccB and ybgT. However, we also identified novel regulation, such as Zur repression of ykgMO, cyclic AMP response protein (CRP) repression of azuC, and CRP activation of ykgR. The levels of 11 small proteins increase after heat shock, and induction of at least 1 of these, YobF, occurs at a posttranscriptional level. These results show that small proteins are an overlooked subset of stress response proteins in E. coli and provide information that will be valuable for determining the functions of these proteins.
authors.affiliation: Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland 20892-5430, USA.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Hemm
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Paul
authors.forename: Juan
authors.initials: J
authors.lastname: Miranda-Ríos
authors.forename: Aixia
authors.initials: A
authors.lastname: Zhang
authors.forename: Nima
authors.initials: N
authors.lastname: Soltanzad
authors.forename: Gisela
authors.initials: G
authors.lastname: Storz
mesh_terms: D000595:Amino Acid Sequence; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D015152:Blotting, Northern; D002373:Cyclic AMP Receptor Protein / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics / Q000502:physiology; D015151:Immunoblotting; D008969:Molecular Sequence Data; D012097:Repressor Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013312:Stress, Physiological
chemical_list: D001425:Bacterial Outer Membrane Proteins; D002373:Cyclic AMP Receptor Protein; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D012097:Repressor Proteins; C114819:Zur protein, E coli; C041610:arcA protein, E coli; C481662:crp protein, E coli