A Phylogenetic Study of sRNA Tpke11 using RNA Secondary Structures

References1. Griffiths-Jones, S, & Bateman, Rfam Database website, A Nucl. Acids Res. 31 (1), p. 439-441, September 2002.2. Fengjie, S, & Caetano-Anollés, G 2009, 'The Evolutionary History of the Structure of 5S Ribosomal RNA', Journal Of Molecular Evolution, 69, 5, p. 430, Advanced Placement Source, viewed 29 November.2014.3. Zeng, Q, & Sundin, G 2014, 'Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function', BMC Genomics, 15, p. 414, MEDLINE with Full Text, EBSCOhost, viewed 29 November 2014.

Small RNAs (sRNA) have many functions in metabolic, regulatory, and catabolic pathways. Small RNAs are found in many different organisms and in all three domains of life. However, many of these non-coding RNA molecules are uncharacterized and their functions are unknown. The RNA molecule tpke11 belongs to a small RNA family with little research conducted. This particular molecule was found theoretically and then found experimentally first in E. coli and a select species of yeast using microarray and Northern blotting techniques. However, many of these species sequences are still only found theoretically and still need to be confirmed in the laboratory. The tpke11 family is involved in gene regulations. This sRNA binds to the chaperone protein Hfq and regulates the translation of sigma 381. Without this sigma factor, RNA polymerase cannot bind to the promoter site and transcription cannot occur. In recent studies it was found that sRNA in Erwinia amylovora is responsible for the fire blight disease in apple and pear. The production of Hfq leads to the binding of RNA polymerase which leads to the synthesis of proteins making this bacteria pathogenic3.

Conclusions• Phylogenetic trees based on RNA sequences showed that the

prokaryotic and eukaryotic species are not revealed in two monophyletic groups.

• Phylogenetic trees based on RNA secondary structures showed that the eukaryotic species could have evolved much more independently from the prokaryotic species.

• The shape of the secondary folding of RNA molecules relates to function and showed that the eukaryotic species evolved independently from that of many prokaryotic species analyzed in this study.

• Future work: A more comprehensive data set should be analyzed in order to support these conclusions drawn from this study.

Experimental Strategy

Samantha Reese (sreese@ggc.edu) and Fengjie Sun (fsun@ggc.edu) School of Science and Technology, Georgia Gwinnett College

AcknowledgementsGeorgia Gwinnett College for travel support

Background

Phylogenetic tree based on structural characters

(Eukayotes are boxed)

Phylogenetic trees based on RNA sequences(Eukaryotes are boxed)

NJ tree

ML tree

MP tree

Coding of RNA secondarystructural characters

MP tree