Variations on the tmRNA gene

Abstract

tmRNA employs both tRNA-like and mRNA-like properties as it rescues stalled bacterial ribosomes, while targeting the defective mRNA and incomplete nascent protein for degradation. We describe variation of the tmRNA gene (ssrA) and how it informs tmRNA structure and function. Endosymbiont tmRNAs tend to lose secondary structure and length in the mRNA-like region as nucleotide composition drifts with that of the whole genome. A dramatic gene structure variation is circular permutation, which produces two-piece tmRNAs in three bacterial lineages; new sequences blur these lineages. We present evidence that Sinorhizobium two-piece tmRNA retains the 5'-triphosphate of transcriptional initiation and predict a new structure at the 5' end of cyanobacterial two-piece tmRNA precursor. ssrA is a target for some mobile DNAs and a passenger on others. It has been found interrupted (but not functionally disrupted) by mobile elements such as group I introns, genomic islands and palindromic elements. The alphaproteobacterial permuted genes are significantly less frequently interrupted by genomic islands than are their standard counterparts, yet are a hotspot for insertion or swapping of rickettsial palindromic elements, in contrast to other rickettsial loci that show steady decay of a single ancestral element. Bacteriophages, plasmids and genomic islands can carry tmRNA genes; we describe a native bacterial ssrA disrupted by insertion of a genomic island that carries its own ssrA, a genome encoding both one-and two-piece tmRNA, and a phage encoding a tmRNA variant lacking the mRNA-like function, which may counteract host tmRNA during infection.

A Rickettsia Genome Overrun by Mobile Genetic Elements Provides Insight into the Acquisition of Genes Characteristic of an Obligate Intracellular Lifestyle

“…The latter two insertion sequences contain Rickettsia palindromic elements (RPEs) (87), and these regions in REIS are highly divergent from comparable regions in other Rickettsia genomes (81). The genes encoding the signal recognition particle RNA (4.5S RNA) and transcription-associated 6S RNA are conserved as in other Rickettsia genomes, although the latter is present twice, as it is encoded within a duplicated region of the genome that contains five ORFs (coordinates 93946 to 101518 and 143906 to 148622) (Fig.…”

A second eukaryotic group with mitochondrion-encoded tmRNA

“…After transcription, the circularly permuted pre-tmRNA is processed, generating two tmRNA fragments. The two halves are held together and arranged in "correct" conformation by RNA base pairing and RNA-binding proteins, 16,17 thus forming the canonical tmRNA secondary structure (Fig. 1B).…”

“…Although based on two-piece molecules with permuted gene sequence, the model also detects the detected in virtually all bacterial genomes. 16,17 In contrast, mitochondrial ssrA genes are currently only known from two unrelated protist groups (for a phylogenetic tree, see Fig. S2).…”

Three years of RNA Families

“…To date, RNA Biology has published nearly 30 RNA Families articles. These have ranged from updates for famous families such as SRP, 3 tmRNA 4 and RNases P and MRP 5,6 through to novel sRNAs, 7-11 snoRNAs 12-15 and viral elements. [16][17][18] We have recently started soliciting reviews of notable miRNA families.…”

“…This illustrates that this series of articles can be a useful way of training research students and can also bridge views spanning research groups that have not traditionally collaborated. 4,12 A number of authors publishing outside the RNA Biology track are now following our criteria. [23][24][25][26][27] This is a very promising sign, indicating that the requirements are not too onerous and the research community can see the benefits of consistently formatted and presented data that can then be used across many different data sets and studies.…”