@article{ellis_thomas_lawson_patel_faircloth_hayes_linton_norden_severenchuk_west_et al._2019, title={Kistimonas alittae sp. nov., a gammaproteobacterium isolated from the marine annelid Alitta succinea}, volume={69}, ISSN={["1466-5034"]}, DOI={10.1099/ijsem.0.003137}, abstractNote={A novel Gram-stain-negative, rod-shaped, motile, non-spore-forming, facultatively anaerobic marine bacterium was isolated from the gastrointestinal tract of the sandworm Alitta succinea collected from Grice Cove, South Carolina, USA. The strain was arginine dihydrolase-positive, and oxidase- and catalase-positive. Growth occurred between 10 and 37 °C, with optimal growth occurring between 30 and 32 °C. Comparative 16S rRNA gene sequence analysis showed its nearest neighbours are members of the genus Kistimonas of the family Hahellaceae, which is found in the order Oceanospirillales, class Gammaproteobacteria. The closest related species was Kistimonas asteriae KMD 001T with 16S rRNA gene sequence similarity of 99.0 %. However, DNA-DNA hybridization between these strains revealed less than 70 % DNA-DNA relatedness, supporting the novel species status of the strain. The major fatty acids were C16 : 0, C18 : 0, C18 : 1ω7c and a summed feature that contained C16 : 1ω6c/C16 : 1ω7c. The major respiratory quinone was ubiquinone-9 and the predominant polar lipids were phosphatidylserine, phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content was 52.5 mol%. Based on the data presented, strain BGP-2T is considered to represent a novel member of the genus Kistimonas, for which the name Kistimonas alittae sp. nov. is proposed. The type strain is BGP-2T (=CCUG 65711T=JCM 30010T).}, number={1}, journal={INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY}, author={Ellis, J. Christopher and Thomas, Michelle Suhan and Lawson, Paul A. and Patel, Nisha B. and Faircloth, Whitney and Hayes, Stephen E. and Linton, Emily E. and Norden, Diana M. and Severenchuk, Irina S. and West, Caitlin H. and et al.}, year={2019}, month={Jan}, pages={235–240} }
 @article{lai_chan_cozen_bernick_brown_gopalan_lowe_2010, title={Discovery of a minimal form of RNase P in Pyrobaculum}, volume={107}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1013969107}, DOI={10.1073/pnas.1013969107}, abstractNote={
            RNase P RNA is an ancient, nearly universal feature of life. As part of the ribonucleoprotein RNase P complex, the RNA component catalyzes essential removal of 5′ leaders in pre-tRNAs. In 2004, Li and Altman computationally identified the RNase P RNA gene in all but three sequenced microbes:
            Nanoarchaeum equitans
            ,
            Pyrobaculum aerophilum
            , and
            Aquifex aeolicus
            (all hyperthermophiles) [Li Y, Altman S (2004)
            RNA
            10:1533–1540]. A recent study concluded that
            N. equitans
            does not have or require RNase P activity because it lacks 5′ tRNA leaders. The “missing” RNase P RNAs in the other two species is perplexing given evidence or predictions that tRNAs are trimmed in both, prompting speculation that they may have developed novel alternatives to 5′ pre-tRNA processing. Using comparative genomics and improved computational methods, we have now identified a radically minimized form of the RNase P RNA in five
            Pyrobaculum
            species and the related crenarchaea
            Caldivirga maquilingensis
            and
            Vulcanisaeta distributa
            , all retaining a conventional catalytic domain, but lacking a recognizable specificity domain. We confirmed 5′ tRNA processing activity by high-throughput RNA sequencing and in vitro biochemical assays. The
            Pyrobaculum
            and
            Caldivirga
            RNase P RNAs are the smallest naturally occurring form yet discovered to function as
            trans
            -acting precursor tRNA-processing ribozymes. Loss of the specificity domain in these RNAs suggests altered substrate specificity and could be a useful model for finding other potential roles of RNase P. This study illustrates an effective combination of next-generation RNA sequencing, computational genomics, and biochemistry to identify a divergent, formerly undetectable variant of an essential noncoding RNA gene.
          }, number={52}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Lai, L. B. and Chan, P. P. and Cozen, A. E. and Bernick, D. L. and Brown, J. W. and Gopalan, V. and Lowe, T. M.}, year={2010}, month={Dec}, pages={22493–22498} }
 @article{tran_brown_maxwell_2004, title={Evolutionary origins of the RNA-guided nucleotide-modification complexes: from the primitive translation apparatus?}, volume={29}, ISSN={0968-0004}, url={http://dx.doi.org/10.1016/j.tibs.2004.05.001}, DOI={10.1016/j.tibs.2004.05.001}, abstractNote={Eukarya and Archaea possess scores of RNA-guided nucleotide-modification complexes that target specific ribonucleotides for 2′-O-methylation or pseudouridylation. Recent characterization of these RNA-modification machines has yielded striking results with implications for their evolutionary origins: the two main classes of nucleotide-modification complex in Archaea share a common ribonucleoprotein (RNP) core element that has evolved from a progenitor RNP. The fact that this common RNP element is also found in ribosomes suggests that the origin of the progenitor RNP lies in the primitive translation apparatus. Thus, the trans-acting, RNA-guided nucleotide-modification complexes of the modern RNP world seem to have evolved from cis-acting RNA or RNP elements contained in the primitive translation apparatus during the transition from the ancient RNA world to the modern RNP world.}, number={7}, journal={Trends in Biochemical Sciences}, publisher={Elsevier BV}, author={Tran, Elizabeth and Brown, James and Maxwell, E.Stuart}, year={2004}, month={Jul}, pages={343–350} }