RNA World Informatics Phylogeny Database

RESEARCH

The overall basic research goal of our group is to understand the early evolution of life. It is our contention that one of the earliest components of the genetic machinery to appear in a form bearing resemblance to its modern equivalent was the ribosome. Dr. Fox first became interested in this matter while he was a postdoctoral research associate with Carl R. Woese at the University of Illinois. At that time, Carl's vision was to utilize historical information in the primary sequences of the ribosomal RNAs (rRNAs) to deduce relationships among extant bacteria. Prior to the advent of rRNA sequence comparisons, determining historical relationships among the different genera of bacteria had been regarded as a largely intractable problem. Early comparisons of 16S rRNAs by cataloging of ribonuclease T1 oligomers showed that bacterial phylogenies were in fact obtainable in this way and by 1980 enough data was available that we were able to publish the first edition of the "Big Tree" which gave an overview of bacterial phylogeny.  The bigger discovery of the existence of a fundamental split in the bacterial world that divides it into what are now known as the Archaea and the Bacteria came in 1977.  In subsequent years, numerous investigators have joined the effort to such an extent that virtually every known bacterial genus has now been examined and placed on the 16S rRNA tree.  At long last, thanks in large part to the efforts of Mitchell L. Sogin, a proper understanding of the evolutionary history of the lower eukaryotes is finally emerging too. Mitch has some nice overview trees on his site
 
With the problem of organism history in its essence solved, Dr. Fox became increasingly interested in the history of the RNA itself. Although the rRNAs were clearly very large at the time of the last common ancestor, they presumably grew from much more modest beginnings, most likely in conjunction with the ribosomal proteins many of which are also clearly very ancient molecules. In order to study the problem of RNA evolution, we are using 5S rRNA and its interaction with three ribosomal proteins (L5, L18 and L25) as a model system. We have developed a plasmid borne mini rRNA operon that encodes a Vibrio proteolyticus 5S rRNA gene whose product is expressed and processed in Escherichia coli. Ten wild type Vibrio 5S rRNAs genes were placed in this expression system and each was found to be potentially valid in the E. coli milieu by virtue of the fact they incorporate at high levels in the active 70S ribosomes without significant impact on cell growth rate. Many variants  of these wild type sequences do not behave in this way and thus can be regarded as likely to be invalid as 5S rRNAs in the E. coli environment. This core experimental system allows us to characterize a portion of the 5S rRNA sequence space in considerable detail. Currently we are undertaking a variety of evolutionary experiments using this system. For example, we are (1) examining apparently equivalent evolutionary paths between points in a sequence space to see if in fact they are equally reasonable; (2) examining common ancestral sequences predicted by parsimony for functional reasonableness; (3) determining by extensive mutagenesis how likely deleterious mutations are and, hopefully, rules to predict them; (4) attempting to develop methods based on a combination of point mutations and extant sequences to identify nonobvious interdependencies in a sequence space; and (5) determining the extent to which functionality of a particular RNA sequence depends on the host environment. In order to better understand the constraints on what determines if an RNA is valid as a 5S rRNA or not, we have also undertaken studies of the 5S rRNA interaction with ribosomal protein L18 and, in conjunction with Xiaolian Gao of our Chemistry Department, NMR studies of 5S rRNA structure.
 
With the ongoing emergence of bacterial genomics as real science, our group has, in collaboration with Susan Martinis, begun to focus on the evolutionary history of the ribosome in toto. This effort is funded by NASA's Exobiology Program and increasing amounts of information on the subject are being made available via our Evolution of Translation Page. We believe that the evolution of the translation machinery may have had its roots in the synthesis of peptide bonds by small aminoacylated RNAs. We have shown that such RNAs can in fact form dipeptides in the presence of small di-peptides (e.g. Ala-His). In examining the structure of various bacterial genomes we found that spatial relationships between genes for various ribosomal components were typically among the most conserved gene arrangements. This suggests that the regulatory elements associated with translation, which are typically at the RNA level,  were among the first to evolve. This is consistent with the emerging prejudice that a RNA genome may have preceded the DNA genome. We are continuing our bioinformatics studies on ribosomal components. We are also collecting knew genome data as well as a result of a collaboration with William R. Widger  in which we are doing extensive sample sequencing on the cyanobacterium Synechoccus PCC-7002 .
 
Like many modern research laboratories, Dr. Fox's also has a more practical focus too. As is well known, the ribosomal RNAs have emerged as attractive targets for identifying or monitoring bacteria in the environment. In collaboration with  Richard C. Willson of the Chemical Engineering Department at the University of Houston  we are currently funded by NASA's National Space Biomedical Research Institute  to develop rRNA based detection systems that can utilizing DNA chip technology that can be used to simultaneously monitor multiple bacterial species in space craft environments. We also collaborate with Duane L. Pierson at NASA's Johnson Space Center  as a result of funding provided by the Institute for Space Systems Operations.
 
The technology that is most uniquely associated with our group, however, is the use of artificial RNAs as a possible monitoring system for genetically modified bacteria. During the course of our work on 5S rRNA, we discovered that certain mutants continued to produce a stable RNA product despite the fact they were no longer incorporated into ribosomes. One of these was a deletion mutant that lacked the entire loop C domain of 5S rRNA. We subsequently created a BstII cloning site in the gene for the deletion RNA such that a novel replacement fragment could be readily cloned back in. The resulting construct is capable of expressing what are in effect artificial RNAs of novel sequence and novel size that accumulate to high levels in the cells carrying them. We believe such RNAs will prove to be subject to growth rate regulation and that it will be possible to use them in monitoring situations as well as in fundamental studies of microbial ecology. With funding from the Environmental Protection Agency's Exploratory Research Program in collaboration with Richard Willson's group we are currently developing an artificial RNA expression system for use in Pseudomonas putida.
 
Dr. Fox's lab is associated with the W. M. Keck Center for Computational Biology and participates in the interdisciplinary Shell Scholars program at the University of Houston. This years Shell topic is global warming.We also are actively involved with researchers at Rice University and the Johnson Space Center to develop an Astrobiology initiative in the Houston area. Interested parties may want to visit the Houston Area  Astrobiology Page or even join our discussion group. Finally, the Fox lab houses the computers behind two bioinformatics facilities, Yellow BAGI and the UH Gene server. These facilities were initiated by Dan Davison when he was on the facuty here at the University of Houston and we are trying to keep them available as long as they are useful.