Small proteins can no longer be ignored

Abstract

Small proteins, here defined as proteins of 50 amino acids or fewer in the absence of processing, have traditionally been overlooked due to challenges in their annotation and biochemical detection. In the past several years, however, increasing numbers of small proteins have been identified either through the realization that mutations in intergenic regions are actually within unannotated small protein genes or through the discovery that some small, regulatory RNAs encode small proteins. These insights, together with comparative sequence analysis, indicate that tens if not hundreds of small proteins are synthesized in a given organism. This review summarizes what has been learned about the functions of several of these bacterial small proteins, most of which act at the membrane, illustrating the astonishing range of processes in which these small proteins act and suggesting several general conclusions. Important questions for future studies of these overlooked proteins are also discussed.

Keywords: cell division; membrane; protein; signal transduction; sporulation; transport.

Figure 1

Sites of small protein action. Depicted is the cytosol of a composite bacterium (Gram-positive or negative) bounded by the plasma membrane (light gray). Subcellular locations or proteins associated with various cell functions are colored as follows: kinases, green; transporters, red; membrane-bound enzymes, blue; cell division septum, yellow; forespore during sporulation, orange; soluble chaperones, purple. Small proteins are depicted as rectangles. Transmembrane small proteins are depicted as rectangles that traverse the plasma membrane; amphipathic helical small proteins that are peripherally membrane associated are drawn as rectangles that are parallel to the plane of the membrane; soluble small proteins are shown in the cytosol.

Figure 2

Phylogenetic distribution of small proteins. Unrooted prokaryotic phylogenetic tree based on 16S rRNA sequences, adapted from Nelson et al. (106). Center: selected major phylogenetic groupings are colored and selected organisms are indicated. Phylogenetic distribution of small proteins discussed in this review are grouped according to biological function and highlighted in red on individual trees shown at lower magnification. Homologs were identified by a PSI_BLAST search of 2262 completely sequenced genomes (as of February 2013). A table summarizing the presence of absence of particular small proteins is given as Supplemental Table 1. This analysis illustrated the disparate nature of small protein annotation; for example, the pmrR gene is annotated in only six out of the 95 genomes in which homologs were found. The alignments of annotated small proteins generated by MUSCLE are given in Supplemental Table 2 and are available in FASTA format at ftp://ftp.ncbi.nih.gov/pub/wolf/_suppl/small.