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      Archaeal and eukaryotic homologs of Hfq : A structural and evolutionary perspective on Sm function

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          Abstract

          Hfq and other Sm proteins are central in RNA metabolism, forming an evolutionarily conserved family that plays key roles in RNA processing in organisms ranging from archaea to bacteria to human. Sm-based cellular pathways vary in scope from eukaryotic mRNA splicing to bacterial quorum sensing, with at least one step in each of these pathways being mediated by an RNA-associated molecular assembly built upon Sm proteins. Though the first structures of Sm assemblies were from archaeal systems, the functions of Sm-like archaeal proteins (SmAPs) remain murky. Our ignorance about SmAP biology, particularly vis-à-vis the eukaryotic and bacterial Sm homologs, can be partly reduced by leveraging the homology between these lineages to make phylogenetic inferences about Sm functions in archaea. Nevertheless, whether SmAPs are more eukaryotic (RNP scaffold) or bacterial (RNA chaperone) in character remains unclear. Thus, the archaeal domain of life is a missing link, and an opportunity, in Sm-based RNA biology.

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          Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

          C Woese, O Kandler, M L Wheelis (1990)
          Molecular structures and sequences are generally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progressively shifted from the organismal to the cellular to the molecular level. Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems--i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy--reflects this primary tripartite division of the living world. To remedy this situation we propose that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would then be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms. (The Eucarya, for example, contain Animalia, Plantae, Fungi, and a number of others yet to be defined). Although taxonomic structure within the Bacteria and Eucarya is not treated herein, Archaea is formally subdivided into the two kingdoms Euryarchaeota (encompassing the methanogens and their phenotypically diverse relatives) and Crenarchaeota (comprising the relatively tight clustering of extremely thermophilic archaebacteria, whose general phenotype appears to resemble most the ancestral phenotype of the Archaea.
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            A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli.

            E Massé, S Gottesman (2002)
            A small RNA, RyhB, was found as part of a genomewide search for novel small RNAs in Escherichia coli. The RyhB 90-nt RNA down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur (Ferric uptake regulator). RyhB RNA levels are inversely correlated with mRNA levels for the sdhCDAB operon, encoding succinate dehydrogenase, as well as five other genes previously shown to be positively regulated by Fur by an unknown mechanism. These include two other genes encoding enzymes in the tricarboxylic acid cycle, acnA and fumA, two ferritin genes, ftnA and bfr, and a gene for superoxide dismutase, sodB. Fur positive regulation of all these genes is fully reversed in an ryhB mutant. Our results explain the previously observed inability of fur mutants to grow on succinate. RyhB requires the RNA-binding protein, Hfq, for activity. Sequences within RyhB are complementary to regions within each of the target genes, suggesting that RyhB acts as an antisense RNA. In sdhCDAB, the complementary region is at the end of the first gene of the sdhCDAB operon; full-length sdhCDAB message disappears and a truncated message, equivalent in size to the region upstream of the complementarity, is detected when RyhB is expressed. RyhB provides a mechanism for the cell to down-regulate iron-storage proteins and nonessential iron-containing proteins when iron is limiting, thus modulating intracellular iron usage to supplement mechanisms for iron uptake directly regulated by Fur.
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              The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae.

              Derrick Lenz, Kenny C Mok, Brendan N Lilley … (2004)
              Quorum-sensing bacteria communicate with extracellular signal molecules called autoinducers. This process allows community-wide synchronization of gene expression. A screen for additional components of the Vibrio harveyi and Vibrio cholerae quorum-sensing circuits revealed the protein Hfq. Hfq mediates interactions between small, regulatory RNAs (sRNAs) and specific messenger RNA (mRNA) targets. These interactions typically alter the stability of the target transcripts. We show that Hfq mediates the destabilization of the mRNA encoding the quorum-sensing master regulators LuxR (V. harveyi) and HapR (V. cholerae), implicating an sRNA in the circuit. Using a bioinformatics approach to identify putative sRNAs, we identified four candidate sRNAs in V. cholerae. The simultaneous deletion of all four sRNAs is required to stabilize hapR mRNA. We propose that Hfq, together with these sRNAs, creates an ultrasensitive regulatory switch that controls the critical transition into the high cell density, quorum-sensing mode.
              Article 0 comments Cited 274 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): RNA Biol
                Journal ID (iso-abbrev): RNA Biol
                Journal ID (publisher-id): RNA
                Title: RNA Biology
                Publisher: Landes Bioscience
                ISSN (Print): 1547-6286
                ISSN (Electronic): 1555-8584
                Publication date (Print): 01 April 2013
                Publication date (Electronic): 01 April 2013
                Publication date PMC-release: 01 April 2013
                Volume: 10
                Issue: 4
                Pages: 636-651
                Affiliations
                [1 ]Department of Chemistry; University of Virginia; Charlottesville, VA USA
                [2 ]Department of Biomolecular Engineering; University of California; Santa Cruz, CA USA
                Author notes
                [* ]Correspondence to: Cameron Mura; Email: cmura@ 123456virginia.edu
                Article
                Publisher ID: 2012RNABIOL0337R Publisher Item ID: 24538
                DOI: 10.4161/rna.24538
                PMC ID: 3710371
                PubMed ID: 23579284
                SO-VID: 90e59d1e-a43b-4944-b3d9-856c11ec1828
                Copyright © Copyright © 2013 Landes Bioscience
                License:

                This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.

                History
                Date received : 18 March 2013
                Date revision received : 29 March 2013
                Date accepted : 03 April 2013
                Categories
                Subject: Special Focus Review

                ScienceOpen disciplines: Molecular biology
                Keywords: sm,lsm,hfq protein,sm fold,oligomers,archaeal rna,rna chaperone,rnp assembly,rnp evolution
                Data availability:
                ScienceOpen disciplines: Molecular biology
                Keywords: sm, lsm, hfq protein, sm fold, oligomers, archaeal rna, rna chaperone, rnp assembly, rnp evolution

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