Publications

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The transfer-messenger RNA (tmRNA) and its partner protein SmpB act together in resolving problems arising when translating bacterial ribosomes reach the end of mRNA with no stop codon. Their genes have been found in nearly all bacterial genomes and in some organelles. The tmRNA Website serves tmRNA sequences, alignments and feature annotations, and has recently moved to http://bioinformatics.sandia.gov/tmrna/. New features include software used to find the sequences, an update raising the number of unique tmRNA sequences from 492 to 1716, and a database of SmpB sequences which are served along with the tmRNA sequence from the same organism.

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

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Genes for the RNA tmRNA and protein SmpB, partners in the trans-translation process that rescues stalled ribosomes, have previously been found in all bacteria and some organelles. We validate recent identification of tmRNA homologs in oomycete mitochondria by finding partner genes from oomycete nuclei that target SmpB to the mitochondrion. Exhaustive search now identifies a small number of complete, often highly derived, bacterial genomes that appear to lack a functional copy of one or the other partner gene (but not both). Three groups with reduced genomes have lost the central loop of SmpB, which is thought to improve alanylation and EF-Tu activation: Carsonella, Hodgkinia and the hemplasmas (hemotropic Mycoplasma). Carsonella has also lost the SmpB C-terminal tail, thought to stimulate the decoding center of the ribosome. Carsonella moreover exhibits gene overlap such that tmRNA maturation should produce a non-stop smpB mRNA, and one isolate exhibits complete degradation of the tmRNA gene yet its smpB shows no evidence for relaxed selective constraint. After loss of the SmpB central loop in the hemoplasmas, a subclade apparently lost tmRNA. At least some of the tmRNA/SmpB-deficient strains appear to further lack the ArfA and ArfB backup systems for ribosome rescue. The most frequent neighbors of smpB are the tmRNA gene, a ratA/rnfH unit, and the gene for RNaseR, a known physical and functional partner of tmRNA-SmpB. The tmRNA Website has moved and been updated, adding an SmpB sequence database (http://bioinformatics.sandia.gov/tmrna).

Lignin is often overlooked in the valorization of lignocellulosic biomass, but lignin-based materials and chemicals represent potential value-added products for biorefineries that could significantly improve the economics of a biorefinery. Fluctuating crude oil prices and changing fuel specifications are some of the driving factors to develop new technologies that could be used to convert polymeric lignin into low molecular weight lignin and or monomeric aromatic feedstocks to assist in the displacement of the current products associated with the conversion of a whole barrel of oil. Our project of understanding microbial lignolysis for renewable platform chemicals aimed to understand microbial and enzymatic lignolysis processes to break down lignin for conversion into commercially viable drop-in fuels. We developed novel lignin analytics to interrogate enzymatic and microbial lignolysis of native polymeric lignin and established a detailed understanding of lignolysis as a function of fungal enzyme, microbes and endophytes. Bioinformatics pipeline was developed for metatranscryptomic analysis of aridland ecosystem for investigating the potential discovery of new lignolysis gene and gene products.

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