TASK DEFINITION: In this task, you're given a paragraph from the research paper and your task is to generate a suitable title for the research paper based on the given paper. Under 100 words is a good title length.
PROBLEM: One sentence summary: CmpA is an OmpA-like protein in Legionella pneumophila that is required for efficient intracellular replication in both primary macrophages and in the environmental host Acanthamoeba castellanii. Editor: Akio Nakane The OmpA-like protein domain has been associated with peptidoglycan-binding proteins, and is often found in virulence factors of bacterial pathogens. The intracellular pathogen Legionella pneumophila encodes for six proteins that contain the OmpA-like domain, among them the highly conserved uncharacterized protein we named CmpA. Here we set out to characterize the CmpA protein and determine its contribution to intracellular survival of L. pneumophila. Secondary structure analysis suggests that CmpA is an inner membrane protein with a peptidoglycan-binding domain at the C-teminus. A cmpA mutant was able to replicate normally in broth, but failed to compete with an isogenic wild-type strain in an intracellular growth competition assay. The cmpA mutant also displayed significant intracellular growth defects in both the protozoan host Acanthamoeba castellanii and in primary bone marrow-derived macrophages, where uptake into the cells was also impaired. The cmpA phenotypes were completely restored upon expression of CmpA in trans. The data presented here establish CmpA as a novel virulence factor of L. pneumophila that is required for efficient intracellular replication in both mammalian and protozoan hosts.

SOLUTION: A conserved OmpA-like protein in Legionella pneumophila required for efficient intracellular replication

PROBLEM: Single-stranded RNA (ssRNA) is the simplest form of genetic molecule and constitutes the genome in some viruses and presumably in primitive life-forms. However, an innate and unsolved problem regarding the ssRNA genome is formation of inactive doublestranded RNA (dsRNA) during replication. Here, we addressed this problem by focusing on the secondary structure. We systematically designed RNAs with various structures and observed dsRNA formation during replication using an RNA replicase (Q␤ replicase). From the results, we extracted a simple rule regarding ssRNA genome replication with less dsRNA formation (less GC number in loops) and then designed an artificial RNA that encodes a domain of the ␤-galactosidase gene based on this rule. We also obtained evidence that this rule governs the natural genomes of all bacterial and most fungal viruses presently known. This study revealed one of the structural design principles of an ssRNA genome that replicates continuously with less dsRNA formation.

SOLUTION: A design principle for a single-stranded RNA genome that replicates with less double-strand formation

PROBLEM: A 28-nucleotide mRNA pseudoknot that overlaps the P1 and P2 genes of sugarcane yellow leaf virus (ScYLV) stimulates −1 ribosomal frameshifting. The in vitro frameshifting efficiency is decreased ≈8 fold upon substitution of the 3′ most loop 2 nucleotide (C27) to adenosine, which accepts a hydrogen bond from the 2′-OH of C14 in stem S1. The solution structures of the wild-type (WT) and the C27A ScYLV RNA pseudoknots show that while the RNAs adopt virtually identical overall structures, there are significant structural differences at the helical junctions of the two RNAs. Specifically, C8 + in loop L1 in the C8 + ·(G12-C28) L1-S2 major groove base triple is displaced by ≈2.3 Å relative to the accepting stem 2 base pair (G12-C28) in the C27A RNA. Here, we employ a double mutant cycle approach to analyze the pairwise coupling of the C8 + ·(G12-C28) and C27·(C14-G7) or A27·(C14-G7) hydrogen bonds in the WT and C27A ScYLV RNAs, respectively, and compare these findings with previous results from the beet western yellows virus (BWYV) RNA. We find that the pairwise coupling free energy (δ AB i ) is favorable for the WT RNA (-0.7 ±0.1 kcal·mol −1 ), thus revealing that formation of these two hydrogen bonds is positively cooperative. In contrast, δ AB i is +0.9 ±0.4 kcal·mol −1 for the poorly functional C27A ScYLV RNA, indicative of non-additive hydrogen bond formation. These results reveal that cooperative hydrogen bond formation across the helical stem junction in H-type pseudoknots correlates with enhanced frameshift stimulation by luteoviral mRNA pseudoknots. pseudoknot; frameshifting; protonated cytidine; hydrogen bond coupling Intricately folded motifs in both the noncoding and coding regions of mRNAs are known to regulate all steps of the translation cycle. RNA functions in cap-independent translational initiation by providing a binding site for 40S ribosomal subunits in internal ribosomal entry sites (IRES) (1). Riboswitches are naturally occurring aptamers that bind metabolites including adenine, guanine, S-adenosylmethionine, and thiamine pyrophosphatase that directly regulate the expression of enzymes linked to their production or degradation (2). Folded RNA motifs found in coding regions of mRNAs regulate ribosomal recoding by stimulating stop codon suppression, stop codon redefinition, or change the translational reading frame, an example of which is −1 programmed ribosomal frameshifting (−1 PRF) (3,4). −1 PRF occurs during translational elongation where the mRNA slips back by one nucleotide into the "−1" reading frame relative to the reference "0" frame. In RNA viruses, −1 PRF is used to produce several †

SOLUTION:
Pairwise coupling analysis of helical junction hydrogen bonding interactions in luteoviral RNA pseudoknots † NIH Public Access Author Manuscript