Patent Publication Number: US-7910307-B2

Title: Eubacterial tmRNA sequences and uses thereof

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     The present application is division of U.S. patent application Ser. No. 11/329,230 filed on 11 Jan. 2006, which in turn in a division of U.S. patent application Ser. No. 09/958,206 filed on 20 Feb. 2002, now U.S. Pat. No. 7,115,366, which in turn is a national stage filing under 35 U.S.C. §371 of International patent application No. PCT/US00/08988 filed on 6 Apr. 2000, which in turn is related to and claims priority under 35 U.S.C. §119(e) to U.S. provisional patent application Ser. No. 60/128,058 filed on 7 Apr. 1999. Each of these applications is incorporated herein by reference. 
    
    
     This application was made with Government support under Grant No. GM 48152, funded by the National Institutes of Health, Bethesda, Md. The Government has certain rights in this invention. 
    
    
     BACKGROUND OF THE INVENTION 
     The present invention is directed to eubacterial tmDNA sequences and the corresponding tmRNA sequences. The present invention is further directed to alignments of eubacterial tmDNA sequences and use of the sequences and sequence alignments for the development of antibacterial drugs. The present invention is also directed to the use of the sequences for the development of diagnostic assays. 
     The publications and other materials used herein to illuminate the background of the invention or provide additional details respecting the practice are incorporated by reference, and for convenience are respectively grouped in the appended List of References. 
     Eubacterial tmRNAs (10Sa RNAs) are unique since they function, at least in  E. coli , both as tRNA and as mRNA (for a review, see Muto et al., 1998). These ≈360±10% nucleotide RNAs are charged with alanine at their 3′-ends (Komine et al., 1994; Ushida et al., 1994) and also have a short reading frame coding for 9 to 27 amino acids depending on the bacterial species.  E. coli  tmRNA mediates recycling of ribosomes stalled at the end of terminatorless mRNAs, via a trans-translation process (Tu et al., 1995; Keiler et al., 1996; Himeno et al., 1997). In  E. coli , this amino acid tag is co-translationally added to polypeptides synthesized from mRNAs lacking a termination codon, and the added 11 amino acid C-terminal tag makes the protein a target for specific proteolysis (Keiler et al., 1996). 
     Structural analyses based on phylogenetic (Felden, et al., 1996; Williams and Bartel, 1996) and probing (Felden et al., 1997; Hickerson et al., 1998) data have led to a compact secondary structure model encompassing 6 helices and 4 pseudoknots. tmRNAs have some structural similarities with canonical tRNAs, especially with tRNA acceptor branches.  E. coli  tmRNA contains two modified nucleosides, 5-methyluridine and pseudouridine, located in the tRNA-like domain of the molecule, in a seven-nucleotide loop mimicking the conserved sequence of T loops in canonical tRNAs (Felden et al., 1998). 
     Fifty-three tmRNA sequences are now known from both experimental data and Blast searches on sequenced genomes (summarized in Williams, 1999; Wower and Zwieb, 1999). These sequences cover only 10 phyla, less than one third of the known bacterial taxa. It is desired to determine additional tmRNA sequences and to use the tmRNA sequences for drug development. 
     SUMMARY OF THE INVENTION 
     The present invention relates to eubacterial tmDNA sequences and the corresponding tmRNA sequences. The present invention further relates to alignments of eubacterial tmDNA sequences and use of the sequences and sequence alignments for the development of antibacterial drugs. 
     In one aspect of the present invention, an extensive phylogenetic analysis was performed. Fifty-eight new tmDNA sequences including members from nine additional phyla were determined. Remarkably, tmDNA sequences could be amplified from all species tested apart from those in the alpha-Proteobacteria. This aspect of the invention allowed a more systematical study of the structure and overall distribution of tmRNA within eubacteria 
     In a second aspect of the invention, alignments are made with the newly isolated tmDNA sequences and previously disclosed tmRNA sequences. 
     In a third aspect of the invention, the alignments of the tmRNA sequences allow the identification of targets for development of antibacterial drugs. 
     In a fourth aspect of the invention, the novel tmDNA or tmRNA sequences of the present invention are used to develop diagnostic assays, such as amplification-based assays, for the bacterial species disclosed herein. 
    
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
         FIGS. 1A-1B  show the effect of the annealing temperature ( FIG. 1A ) and magnesium concentration ( FIG. 1B ) on amplifying eubacterial tmRNA genes from genomic DNAs using PCR. A: Varying the annealing temperature from 50° to 70° C. during the PCR amplification of  Thermus aquaticus  (1). B; Varying the magnesium concentration to amplify tmDNA genes from  Thermus aquaticus  (1), negative effect of increasing the magnesium concentration),  Acholeplasma laidlawii  (2), positive effect of increasing the magnesium concentration, the upper band is the tmDNA gene) and from  Mycoplasma salivarium  (3), no discernible effect of magnesium ions in that concentration range). The arrows point toward the 4 novel tmDNA genes that have been sequenced. 
         FIG. 2  shows the distribution of tmDNA sequences within eubacterial genomes. The circled phyla or subgroups contain tmDNA sequences and those shaded are new members of this category. The numbers shown close to each phylum are the 51 tmDNA sequences that have are disclosed herein and the numbers in parenthesis are the 53 tmDNA sequences that were previously known (summarized in Williams, 1999; Wower and Zwieb, 1999). The environmental samples are indicated with a dashed line as their connection to the tree is unknown. The 5 alpha-Proteobacteria in which tmDNA sequences were not detected by PCR analysis are labeled “PCR” and the 3 analyzed by Blast search of the complete, or nearly complete, sequenced genomes are labeled “database”. 
         FIGS. 3A ,  3 B and  3 C show the sequence alignment, structural domains and structural features for the tmRNA of several species of Firmicutes. The tmRNA sequences are set forth in SEQ ID NOs:67-87. 
         FIGS. 4A and 4B  show the sequence alignment, structural domains and structural features for the tmRNA of several species of Thermophiles. The tmRNA sequences are set forth in SEQ ID NOs:88-99. 
         FIGS. 5A and 5B  show the sequence alignment, structural domains and structural features for the tmRNA of several species of Cyanobacteries ( 5 A) and chloroplasts ( 5 B). The tmRNA sequences of the Cyanobacteries are set forth in SEQ ID NOs:100-103, and the tmRNA sequences of the chloroplasts are set forth in SEQ ID NOs:104-108. 
         FIGS. 6A and 6B  show the sequence alignment, structural domains and structural features for the tmRNA of several species of Mycoplasmes. The tmRNA sequences are set forth in SEQ ID NOs:109-117. 
         FIGS. 7A-1 ,  7 A- 2 ,  7 B,  7 C and  7 D show the sequence alignment, structural domains and structural features for the tmRNA of several species of Mesophiles ( 7 A- 1 ,  7 A- 2 ,  7 C,  7 D) and environmental sludge ( 7 B). The tmRNA sequences of the Mesophiles are set forth in SEQ ID NOs:118-123 and 125-128, and the tmRNA sequence of the environmental sludge is set forth in SEQ ID NO:124. The tmRNA sequences of several species of  Chlamydia  are set forth in SEQ ID NOs:129-131. 
         FIGS. 8A and 8B  show the sequence alignment, structural domains and structural features for the tmRNA of several species of Actinobacteries ( 8 A) and Spirochaetes ( 8 B). The tmRNA sequences of the Actinobacteries are set forth in SEQ ID NOs:132-136, and the tmRNA sequences of the Spirochaetes are set forth in SEQ ID NOs:137-142. 
         FIGS. 9A and 9B  show the sequence alignment, structural domains and structural features for the tmRNA of several species of Pourpres beta. The tmRNA sequences are set forth in SEQ ID NOs:143-154. 
         FIGS. 10A ,  10 B and  10 C show the sequence alignment, structural domains and structural features for the tmRNA of several species of Pourpres gamma. The tmRNA sequences are set forth in SEQ ID NOs:155-169. 
         FIGS. 11A and 11B  show the sequence alignment, structural domains and structural features for the tmRNA of several species of Pourpres delta ( 11 A) and Pourpres epsilon ( 11 B). The tmRNA sequences of the Pourpres delta are set forth in SEQ ID NOs:170-172, and the tmRNA sequences of the Pourpres epsilon are set forth in SEQ ID NOs:173-175. 
     
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     The present invention is directed to eubacterial tmDNA sequences and the corresponding tmRNA sequences. The present invention is further directed to alignments of eubacterial tmDNA sequences and use of the sequences and sequence alignments for the development of antibacterial drugs. 
     The novel eubacterial tmDNA sequences determined in accordance with the present invention are set forth in Tables 1-58, below. The alignment of tmRNA sequences is shown in  FIGS. 3A-11B , which also show the structural domains and structural features of the tmRNA. The present invention also includes the tmRNA sequences set forth in these figures to the extent they differ from the sequences set forth in Tables 1-58. 
     The sequences, especially as identified by the sequence alignment, represent targets for the development of drugs which may be broadly applicable to many kinds of bacteria, or may be broadly applicable only to a particular genera of phylum of bacteria, or may be specifically applicable to a single species of bacteria. Thus, the present invention is further directed to the development of drugs for the therapeutic treatment of bacteria, generically or specifically. Suitable drugs are developed on the basis of the tmRNA sequences as described herein. 
     For all the novel tmRNA sequences, as well as with the ones that are already known, there are systematically several structural domains that are always found. These domains can be used as targets for the development of drugs which may be genera specific or which may be eubacteria specific. These domains are either RNA helices which can be sometimes interrupted by bulges or pseudoknots. The RNA helices which are always present are H1, H2, H5 and H6. Helices H1 and H6 are found in all canonical transfer RNAs. Thus, H1 and H6 are not good targets for drug development because drugs that would target them will also interfere with the biology of the individual that has a given disease. Consequently, very good candidates for development of drugs for targeting as many bacteria as possible are helices H2 and H5. Moreover, helices H2 and H5 are critical for the folding of all these tmRNA since both of them connect the two ends of the molecule together. Disruption of either H2 or H5 with a specific drug would lead to inactive tmRNA molecules in vivo. Similarly, pseudoknots PK1, PK2 and PK3 are always found in the bacterial tmRNAs. Since these pseudoknots are not found in all canonical transfer RNAs, they can also be targeted with specific drugs. Disruption of either PK1 or PK2 or PK3 with a specific drug would lead to inactive tmRNA molecules in vivo. 
     In addition to developing drugs which broadly target many bacteria, drugs are developed which are more genera specific. For trying to target specifically a given bacteria or a complete phylum, the coding sequence (shown in all the alignments) is a very good candidate. Indeed, this region of the RNA is very accessible for DNA antisense binding (such as shown for  Escherichia coli ; Matveeva et al., 1997), and thus, is also available for interaction with other drugs. Moreover, the coding sequence is a critical functional domain of the molecule in its quality-control mechanism in cells. 
     Interestingly, some structural domains are present only in a given bacterial phyla and could be targeted for discovering a drug that will be specific of a phylum, but not of the others. For example: 
     (1) in the cyanobacteria, the fourth pseudoknot PK4 is made of two smaller pseudoknots called PK4a and PK4b; 
     (2) in the mycoplasma, helix H2 is made of only 4 base-pairs instead of 5 in the other species; 
     (3) for two sequences of chlorobium as well as  Bacteroides thetaiotaomicron  and ppm gingiv., there is an additional domain just downstream of the coding sequence that is unique to them; 
     (4) there is always a stem-loop in the coding sequence of the actinobacteria (Felden et al., 1999); and 
     (5) all the beta proteobacteria possess a sequence insertion in pseudoknot PK2 (shown in the alignment). 
     The novel sequences described herein, when aligned, show that specific structural domains within tmRNA are strictly conserved, as for example pseudoknot PK1 is located upstream (at the 5′-side) of the coding sequence. As previously disclosed, this pseudoknot is a target for future anti-bacterial drugs. Moreover, recent data have shown that this PK1 pseudoknot, among all the four pseudoknots within tmRNA gene sequences (sometimes there&#39;s only 2 or 3 detectable pseudoknots, depending upon the sequences), is the only one that its correct folding is essential for the biological activity of tmRNA (Nameki et al., 1999; Nameki et al., 2000). 
     It has recently been discovered that even the alpha-proteobacteria possess tmRNA genes. These genes are permuted and are made in two parts, connected via a processed linker. These tmRNA gene sequences from alpha-proteobacteria were not found in the course of the present invention because usual PCR methods could not amplify them. 
     Recent reports have shown that whereas the gene encoding tmRNA is non-essential in  E. coli  (does not kill the bacteria when disrupted), it is indeed essential in  Neisseria gonorrheae  (Huang et al., 2000). Also, tmRNA is directly involved in  Salmonella typhymurium  pathogenticity (Julio et al., 2000). 
     In summary, tmRNA genes are present in all eubacterial genomes, with no exceptions, but are not present in any genomes from archebacteries or eukaryotes, with the exception of some chloroplasts. The very specific location of tmRNA genes within one of the three main kingdoms of life make them ideal targets for the design of novel antibiotics that will, in principle, interfere very weakly with human biochemistry, compared to usual antibiotics. For a recent review about designing novel antibiotics, see Breithaupt (1999). 
     The present invention is also directed to diagnostic assays and kits for the detection of bacterial infection, particularly infections caused by bacterial agents disclosed herein. In one embodiment, the coding sequence of each bacterial species is used to design specific primers for use in amplification-based diagnostic assays for infectious diseases. Specific primers are designed in accordance with well known techniques, and such design is readily done by a skilled artisan. Amplification-based diagnostic assays are performed in accordance with conventional techniques well known to skilled artisans. Examples of amplification-based assays include, but are not limited to, polymerase chain reaction (PCR) amplification, strand displacement amplification (SDA), ligase chain reaction (LCR) amplification, nucleic acid sequence based amplification (3SR or NASBA) and amplification methods based on the use of Q-beta replicase. 
     Drugs which target the sequences described herein are active agents can be formulated in pharmaceutical compositions, which are prepared according to conventional pharmaceutical compounding techniques ( Remington&#39;s,  1990). The composition may contain the active agent or pharmaceutically acceptable salts of the active agent. These compositions may comprise, in addition to one of the active substances, a pharmaceutically acceptable excipient, carrier, buffer, stabilizer or other materials well known in the art. Such materials should be non-toxic and should not interfere with the efficacy of the active ingredient. The carrier may take a wide variety of forms depending on the form of preparation desired for administration, e.g., intravenous, oral, intrathecal, epineural or parenteral. 
     For oral administration, the compounds can be formulated into solid or liquid preparations such as capsules, pills, tablets, lozenges, melts, powders, suspensions or emulsions. In preparing the compositions in oral dosage form, any of the usual pharmaceutical media may be employed, such as, for example, water, glycols, oils, alcohols, flavoring agents, preservatives, coloring agents, suspending agents, and the like in the case of oral liquid preparations (such as, for example, suspensions, elixirs and solutions); or carriers such as starches, sugars, diluents, granulating agents, lubricants, binders, disintegrating agents and the like in the case of oral solid preparations (such as, for example, powders, capsules and tablets). Because of their ease in administration, tablets and capsules represent the most advantageous oral dosage unit form, in which case solid pharmaceutical carriers are obviously employed. If desired, tablets may be sugar-coated or enteric-coated by standard techniques. The active agent can be encapsulated to make it stable to passage through the gastrointestinal tract while at the same time allowing for passage across the blood brain barrier. See for example, WO 96/11698. 
     For parenteral administration, the compound may dissolved in a pharmaceutical carrier and administered as either a solution of a suspension. Illustrative of suitable carriers are water, saline, dextrose solutions, fructose solutions, ethanol, or oils of animal, vegetative or synthetic origin. The carrier may also contain other ingredients, for example, preservatives, suspending agents, solubilizing agents, buffers and the like. When the compounds are being administered intrathecally, they may also be dissolved in cerebrospinal fluid. 
     The active agent is preferably administered in an therapeutically effective amount. The actual amount administered, and the rate and time-course of administration, will depend on the nature and severity of the condition being treated. Prescription of treatment, e.g. decisions on dosage, timing, etc., is within the responsibility of general practitioners or specialists, and typically takes account of the disorder to be treated, the condition of the individual patient, the site of delivery, the method of administration and other factors known to practitioners. Examples of techniques and protocols can be found in  Remington&#39;s Pharmaceutical Sciences  (18). 
     Alternatively, targeting therapies may be used to deliver the active agent more specifically to certain types of cell, by the use of targeting systems such as antibodies or cell-specific ligands. Targeting may be desirable for a variety of reasons, e.g. if the agent is unacceptably toxic, or would otherwise require too high a dosage, or otherwise be unable to enter the target cells. 
     Antisense active agents can also be delivered by techniques described in U.S. Pat. Nos. 5,811,088; 5,861,290 and 5,767,102. 
     EXAMPLES 
     The present invention is further detailed in the following Examples, which are offered by way of illustration and are not intended to limit the invention in any manner. Standard techniques well known in the art or the techniques specifically described below are utilized. 
     Example 1 
     Materials and Methods 
     1. Extraction of Genomic DNA 
     Bacterial genomic DNAs were prepared from ≈10 mg freeze-dried cells provided from ATCC (American Type Culture Collection, Virginia, USA). Cell pellets were resuspended in 750 μL of lysis buffer (50 mM Tris (pH 8.0), 50 mM EDTA and 20% sucrose). 150 μL of a 10 mg/mL solution of lysozyme was mixed and let stand at room temperature for 15 min. 150 μL of 1% SDS was added and let stand at room temperature for 15 minutes. Four to five phenol/chloroform extractions were performed, until the sample was clear and there was no interphase. Two to five μL of a 10 mg/mL solution of RNase DNase-free was added and incubated at room temperature for 30 minutes. After a phenol/chloroform extraction of the enzyme, the genomic DNA was precipitated with 1/10 volume of 3M NaOAc (pH 5.5) and 1 volume isopropanol, and stored at −20° C. for 2 hours. After centrifugation, the genomic DNAs were washed with 70% ethanol, vacuum-dried and diluted in sterile water to a final concentration of 10 ng/μL. 
     2. Primer Sets for PCR Reactions 
     The following primer sets were used during the PCR:
         primer set A (based on  E. coli  tmRNA termini):       

     
       
         
           
               
               
            
               
                 5′-GGG GCT GAT TCT GGA TTC GAC-3′ 
                 (SEQ ID NO: 1) 
               
               
                 and 
                   
               
               
                   
               
               
                 5′-TGG AGC TGG CGG GAG TTG AAC-3′; 
                 (SEQ ID NO: 2) 
               
            
           
         
       
         
         
           
             primer set B (based on  T. neapolitana  tmRNA termini): 
           
         
       
    
     
       
         
           
               
               
            
               
                 5′-GGG GGC GGA AAG GAT TCG ACG-3′ 
                 (SEQ ID NO: 3) 
               
               
                 and 
                   
               
               
                   
               
               
                 5′-TGG AGG CGG CGG GAA TCG AAC-3′; 
                 (SEQ ID NO: 4) 
               
            
           
         
       
         
         
           
             primer set C (based on  M. pneumoniae  tmRNA termini): 
           
         
       
    
     
       
         
           
               
               
            
               
                 5′-GGG GAT GTC ATG GTT TTG ACA-3′ 
                 (SEQ ID NO: 5) 
               
               
                 and 
                   
               
               
                   
               
               
                 5′-TGG AGA TGG CGG GAA TCG AAC-3′; 
                 (SEQ ID NO: 6) 
               
               
                 and 
                   
               
            
           
         
       
         
         
           
             primer set D (based on  C. tepidum  tmRNA termini): 
           
         
       
    
     
       
         
           
               
               
            
               
                 5′-GGG GAT GAC AGG CTA TCG ACA-3′ 
                 (SEQ ID NO;7) 
               
               
                 and 
                   
               
               
                   
               
               
                 5′-TGG AGA TGG CGG GAC TTG AAC-3′. 
                 (SEQ ID NO: 8) 
               
            
           
         
       
     
     3. PCR Reaction 
     Sequences of tmRNA genes were obtained by polymerase chain reaction (PCR) in 25 μL using 40 ng of genomic DNA per reaction. The following general scheme was utilized for all of the sequences: 
     (a) 94° C. to 96° C. for 4 min. (first denaturation of genomic DNAs, done only once); then 
     (b) 35 to 40 PCR cycles with 2.5 to 5 Units of Taq DNA polymerase in a 25 μL reaction volume, according to the following scheme (40 ng of genomic DNAs/PCR reaction):
         1. denature at 94° to −96° C. for 25 to 30 sec;   2. anneal at 44° to 55° C. for 20 to 30 sec; and   3. extension at 72° C. for 10 sec.
 
The magnesium conc. was optimized for each phyla from 3.5 to 13.5 mM.
       

     4. Elution of Amplified DNAs 
     The various PCR-amplified tmDNA bands were gel purified (5% PAGE), stained (ethidium bromide staining), cut using a sterile razor blade, and shaken over-night (passive elution, using a vibrator) in a 350 μl solution containing 10 mM Tris-HCl buffer (pH 8.1). The following day, the PCR amplified tmDNAs were ethanol precipitated, washed in 70% ETOH, vacuum dried and the DNA pellets were dissolved in 18 μl of RNase-DNase free sterile water. 
     5. DNA Sequencing 
     Six μL of amplified DNAs were added to 3.2 picomoles of the primer that was used in the PCR. To verify the novel tmDNA sequences, each of the two primers were used independently to sequence each of the two PCR-amplified DNA strands. Some tmDNAs were already engineered at their 5′-ends with a T7 promoter, to be able to transcribe directly the tmDNAs into tmRNAs by in vitro transcription. 
     Dye terminator sequencing was achieved at the DNA sequencing facility of the Human Genetics Institute. In addition to novel tmRNA sequences that are not available publicly, several tmDNA sequences that were already known have been verified and several sequencing mistakes have been found and corrected (especially for  Alcaligenes eutrophus  tmRNA). 
     Example 2 
     Amplification Reactions for Eubacterial tmDNA 
     Eubacterial tmDNA was amplified by PCR in accordance with Example 1, using the following conditions. 
     
       Acidobacterium:  
     
     Primer Set B; Annealing temp. during PCR: 53° C. for 20 sec; Mg 2+  conc.: 4.5 mM. 
     
       Coprothermobacter:  
     
     Primer Set B; Annealing temp. during PCR: 55° C. for 30 sec; Mg 2+  conc.: 5.5 mM. 
     Cytophagales: 
     Primer Set A; Annealing temp. during PCR: 46° C. for 30 sec; Mg 2+  conc.: 4.5 mM. 
     
       Dictyoglomus:  
     
     Primer set B; Annealing temp. during PCR: 55° C. for 30 sec; Mg 2+  conc.: 4.5 mM. 
     Environmental Samples: 
     Sludge DNA 
     Primer set C; Annealing temp. during PCR: 51° C. for 20 sec; Mg2+  conc.: 13.5 mM. 
     Rumenal Fluid DNA 
     Primer set D; Annealing temp. during PCR: 50° C. for 30 sec; Mg 2+  conc.: 9.5 mM. 
     
       Fibrobacter:  
     
     Primer set A; Annealing temp. during PCR: 51° C.; Mg 2+  conc.: 3.5 mM. 
     Firmicutes: 
     Fusobacteria: 
     Primer set A; Annealing temp. during PCR: 52° C.; Mg 2+  conc.: 5.5 mM. 
     High G-C: 
     Primer set A; Annealing temp. during PCR: 50-55° C.; Mg 2+  conc.: 4.5 mM. 
     Low G-C: 
     Primer sets A or B; Annealing temp. during PCR: 52° C.; Mg 2+  conc.: 5.5 to 7.5 mM. 
     Mycoplasmes: 
     Primer set A; Annealing temp. during PCR: 52° C.; Mg 2+  conc.: 3.5 to 5.5 mM. 
     Green Non-Sulfur: 
     Primer sets A or B; Annealing temp. during PCR: 46 to 52° C.; Mg 2+  conc.: 4.5 mM. 
     Green Sulfur: 
     Primer set A; Annealing temp. during PCR: 46° C.; Mg 2+  conc.: 4.5 mM. 
     Planctomycetales: 
     Primer set A; Annealing temp. during PCR: 48 to 52° C.; Mg 2+  conc.: 7.5 mM. 
     Proteobacteria: 
     beta: 
     Primer sets A and/or B; Annealing temp. during PCR: 50° C. for 25 sec; Mg 2+  conc.: 3.5 mM. 
     delta: 
     Primer set B; Annealing temp. during PCR: 55° C.; Mg 2+  conc.: 3.5 to 4.5 mM. 
     epsilon: 
     Primer set A; Annealing temp. during PCR: 46° C. for 30 sec; Mg 2+  conc.: 3.5 mM. 
     gamma: 
     Primer set A; Annealing temp. during PCR: 44 C for 30 sec; Mg 2+  conc.: 5.5 mM. 
     Spirochetes: 
     Primer set A; Annealing temp. during PCR: 52° C.; Mg 2+  conc.: 4.5 mM. 
     
       Thermodesulfobacterium:  
     
     Primer set B; Annealing temp. during PCR: 55° C.; Mg 2+  conc.: 5.5 mM. 
     Thermotogales: 
     Primer set B; Annealing temp. during PCR: 46° C.; Mg 2+  conc.: 7.5 mM. 
     Deinococcales: 
     Primer set B; Annealing temp. during PCR: 52° C.; Mg 2+  conc.: 3.5 mM. 
     Verrucomicrobia: 
     Primer set A; Annealing temp. during PCR: 53° C. for 25 sec; Mg 2+  conc.: 3.5 mM. 
     Example 3 
     Amplification of Eubacterial tmDNA 
     Specific PCR amplification of tmRNA genes was achieved for both thermophilic and mesophilic eubacterial tmRNA genes. For the novel tmDNA genes found in thermophiles, both the magnesium concentration and the annealing temperature ( FIG. 1A ) were optimized. As shown in  FIG. 1A , a specific amplification of  Thermus aquaticus  tmDNA was observed with an annealing temperature around 50° C., whereas at higher temperatures there is a gradual decrease in the amount of amplified tmDNA. For mesophiles, the magnesium concentration during PCR was critical ( FIG. 1B ), but the annealing temperature could vary from 44° C. to 60° C. without significant effects on the amplification.  FIG. 1B  shows various effects of increasing the magnesium concentration on the PCR amplification of three novel eubacterial tmDNA genes. Increasing magnesium concentration from 3.5 mM to 5.5 mM has either a negative ( FIG. 1B , panel 1), a positive ( FIG. 1B , panel 2) or no effect on specifically amplifying eubacterial tmDNA genes. 
     According to these procedures, tmRNA genes from many eubacteria including known human pathogens were amplified. The PCR was facilitated by sequence conservation at both 5′ and 3′ ends and was performed as described (Williams and Bartel, 1996), with modifications. This study was initiated to collect further sequences from eubacterial tmDNA genes, as well as to test experimentally whether tmDNA genes could be found in all bacterial phyla or subgroups. 51 new tmDNA sequences were determined ( FIG. 2 ), including sequences from members of 8 additional phyla and 1 subgroup (shaded boxes in  FIG. 2 ). The 58 new tmDNA sequences are set forth in Tables 1-58. This brings coverage to a total of 104 sequences in 19 bacterial phyla. Interestingly, tmDNA sequences could be amplified from all species tested apart from those in the alpha-Proteobacteria. Five genomic DNAs from alpha-Proteobacteria ( Agrobacterium tumefaciens, Bartonella henselae, Bartonella quintana, Rhodospirillum rubrum  and  Rickettsia prowazekii ) were extensively checked using various oligonucleotides, annealing temperatures and magnesium concentrations. No specific amplified tmDNA sequences were detected in this subgroup. Moreover, no putative tmDNA sequences could be identified (results herein and Williams, 1999) by Blast searches on the 1 fully sequenced ( Rickettsia prowazekii ) and 2 nearly completed ( Caulobacter crescentus  and  Rhodobacter capsulatus ) alpha-proteobacterial genomes ( FIG. 2 ). 
     It cannot be ruled out that tmDNA sequences may have largely diverged in the alpha-proteobacterial sub-group compared to other bacterial phyla, and that both PCR methods and Blast searches are missing the relevant sequences. While tmRNA is dispensable in  E. coli  (Ando et al., 1996), it is striking that it has been found in all bacteria tested other than the alpha-Proteobacteria. The alpha-Proteobacteria have undergone reductive evolution. This has been more intensive in one of the two sub-classes than in the other (Gray and Spencer, 1996), but tmRNA sequences have not been found even in the sub-class with the larger genome. Based on sequence comparison, the alpha-Proteobacteria and mitochondria are evolutionary relatives (Yang et al., 1985; Andersson et al., 1998). The drastic downsizing in what has become mitochondrial genomes means that it is not reasonable to draw inferences on the relationship between alpha-Proteobacteria and mitochondria based on their mutual apparent absence of tmRNA. It is nevertheless, of interest, that at least some chloroplasts and cyanelle genomes have tmDNA sequences, and the cyanobacteria, with which they are evolutionary related, also have tmRNA. 
     
       
         
           
               
             
               
                 TABLE 1 
               
               
                   
               
               
                 tmDNA Sequence for  Acidobacterium capsulatum   
               
               
                 ( Acidobacterium ) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 9) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGTTGACTGCGGCAAAGAGGCATGCCGG 
               
               
                 GGGGTGGGCACCCGTAATCGCTCGCAAAACAATACTTGCCAACAACAATC 
               
               
                 TGGCACTCGCAGCTTAATTAAATAAGTTGCCGTCCTCTGAGGCTTCGCCT 
               
               
                 GTGGGCCGAGGCAGGACGTCATACAGCAGGCTGGTTCCTTCGGCTGGGTC 
               
               
                 TGGGCCGCGGGGATGAGATCCACGGACTAGCATTCTGCGTATCTTGTCGC 
               
               
                 TTCTAAGCGCAGAGTGCGAAACCTAAAGGAATGCGACTGAGCATGGAGTC 
               
               
                 TCTTTTCTGACACCAATTTCGGACGCGGGTTCGATTCCCGCCGCCTCCAC 
               
               
                 CA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2 
               
               
                   
               
               
                 tmDNA Sequence for  Coprothermobacter proteolyticus   
               
               
                 (60 degrees) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 10) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGAGTCGGAGCCTTGAGCTGCAGGCAGG 
               
               
                 GTTGGCTGCCACACCTTAAAAAGGGTAGCAAGGCAAAAATAAATGCCGAA 
               
               
                 CCAGAATTTGCACTAGCTGCTTAATGTAAGCAGCCGCTCTCCAAACTGAG 
               
               
                 GCTGCATAAGTTTGGAAGAGCGTCAACCCATGCAGCGGCTCTTAAGCAGT 
               
               
                 GGCACCAGCTGTTTAAGGGTGAAAAGAGTGGTGCTGGGCAGTGCGGTTGG 
               
               
                 GCTTCCTGGGCTGCACTGTCGAGACTTCACAGGAGGGCTAAGCCTGTAGA 
               
               
                 CGCGAAAGGTGGCGGCTCGTCGGACGCGGGTTCGATTCCCGCCGCCTCCA 
               
               
                 CCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
               
                   
               
               
                 tmDNA Sequence for  Bacteroides thetaiotaomicron   
               
               
                 ( bacteroides / flavobacterium ) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 11) 
               
               
                 GGGGCTGATTCTGGATTCGACAGCGGGCAGAAATGGTAGGTAAGCATGCA 
               
               
                 GTGGGTCGGTAATTTCCACTTAAATCTCAGTTATCAAAACTTTATCTGGC 
               
               
                 GAAACTAATTACGCTCTTGCTGCTTAATCGAATCACAGTAGATTAGCTTA 
               
               
                 ATCCAGGCACTAGGTGCCAGGACGAGACATCACTCGGAAGCTGTTGCTCC 
               
               
                 GAAGCATTCCGGTTCAGTGGTGCAGTAACATCGGGGATAGTCAGAAGCGG 
               
               
                 CCTCGCGTTTTTGATGAAACTTTAGAGGATAAGGCAGGAATTGATGGCTT 
               
               
                 TGGTTCTGCTCCTGCACGAAAATTTAGGCAAAGATAAGCATGTAGAAAGC 
               
               
                 TTATGATTTCCTCGTTTGGACGAGGGTTCAACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
               
                   
               
               
                 tmDNA Sequence for  Dictyoglomus thermophilum   
               
               
                 (70 degrees) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 12) 
               
               
                 GGGGCTGATTCTGGATTCGACAGGGAGTACAAGGATCAAAAGCTGCAAGC 
               
               
                 CGAGGTGCCGTTACCTCGTAAAACAACGGCAAAAAAGAAGTGCCAACACA 
               
               
                 AATTTAGCATTAGCTGCTTAATTTAGCAGCTACGCTCTTCTAACCCGGGC 
               
               
                 TGGCAGGGTTAGAAGGGTGTCATAATGAGCCAGCTGCCCCTTCCGACTCC 
               
               
                 CCTAAGGAAGGGAAAGATGTAGGGGATAGGTGCTTACAGAATCCTGCGGG 
               
               
                 AGGGAGTCTGTAAGTGCCGAAAAGTTAAAACTCCCGCTAAGCTTGTAGAG 
               
               
                 GCTTTTGATTCTTGCTCTCTGGACGCGGGTTCAACTCCCGCCAGCTCCAC 
               
               
                 CA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5 
               
               
                   
               
               
                 tmDNA Sequence for Environmental Sample 
               
               
                 from Rumenal Fluid 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 13) 
               
               
                 ACGCCCTTGTCTCAGACGAGGGCACTCGTTAAAAAGTCTGAAAAGAATAA 
               
               
                 CTGCAGAACCTGTAGCTATGGCTGCTTAATTTAAGGGCAACCCTTGGATC 
               
               
                 CGCCTCCATCCCGAAGGGGTGGCATCCGAGTCGCAAATCGGGATAGGATG 
               
               
                 GATCTTGGCAACGAGGAGTACATCCGAAATTTGTCGCTGCTGGCTGAAGC 
               
               
                 ATCGCCGTTCCTCTTTGGGCGTGGCAAGGCAAGATTAAATTCAGAGGATA 
               
               
                 AGCGTGTAGTAGCGAGTGAGTAGGTGTTTTTGGACGCGGGTTCAAGTCCC 
               
               
                 GCCATCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 6 
               
               
                   
               
               
                 tmDNA Sequence for Environmental 
               
               
                 Sample from Sludge 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 14) 
               
               
                 GGGGATGTCATGGTTTTGACAGGGAACCAGGAGGTGTGAGATGCATGCCG 
               
               
                 GAGACGCTGTCCGCTCCGTTATCAAGCAGCAAACAAAACTAATTGCAAAC 
               
               
                 AACAATTACTCCTTAGCAGCGTAAGCAGCTAACGTTCAACCTCTCCGGAC 
               
               
                 CGCCGGGAGGGGATTTGGGCGTCGAAACAGCGCGGACGCTCCGGATAGGA 
               
               
                 CGCCCATAATATCCGGCTAAGACCATGGGTCTGGCTCTCGCGGGTCTGAT 
               
               
                 TGTCTTCCACCGCGCGGGCCGCGATCAAAGACAACTAAGCATGTAGGTTC 
               
               
                 TTGCATGGCCTGTTCTTTGGACGCGGGTTCGATTCCCGCCATCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 7 
               
               
                   
               
               
                 tmDNA Sequence for  Fibrobacter succinogenes   
               
               
                 ( Fibrobacter ) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 15) 
               
               
                 GGGGCTGATTCTGGATTCGACAGGGTTACCGAAGTGTTAGTTGCAAGTCG 
               
               
                 AGGTCTCAGACGAGGGCTACTCGTTAAAAAGTCTGAAAAAAAATAAGTGC 
               
               
                 TGACGAAAACTACGCACTCGCTGCCTAATTAACGGCAACGCCGGGCCTCA 
               
               
                 TTCCGCTCCCATCGGGGTGTACGTCCGGACGCAATATGGGATAGGGAAGT 
               
               
                 GTCATGCCTGGGGGCATCTCCCGAGATTTTCTAGGCTGGTCAAACTCCGC 
               
               
                 GCCGACCTTCTTGGGCGTGGATAAGACGAGATCTTAAATTCGAAGGGAAC 
               
               
                 ACTTGTAGGAACGTACATGGACGTGATTTTGGACAGGGGTTCAACTCCCG 
               
               
                 CCAGCTCCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 8 
               
               
                   
               
               
                 tmDNA Sequence for  Fusobacterium mortiferum   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 16) 
               
               
                 GGGGCTGATTCTGGATTCGACGGGGTTATGAGGTTATAGGTAGCATGCCA 
               
               
                 GGATGACCGCTGTGAGAGGTCAACACATCGTTTAGATGGAAACAGAAATT 
               
               
                 ACGCTTTAGCTGCTTAATTAGTCAGCTCACCTCTGGTTTCTCTCTTCTGT 
               
               
                 AGGAGAATCCAACCGAGGTGTTACCAATATACAGATTACCTTTAGTGATT 
               
               
                 TCTCTAAGCTCAAAGGGACATTTTAGAGAATAGCTTCAGTTAGCCCTGTC 
               
               
                 TGCGGGAGTGATTGTTGCGAAATAAAATAGTAGACTAAGCATTGTAGAAG 
               
               
                 CCTATGGCGCTGGTAGTTTCGGACACGGGTTCAACTCCCGCCAGCTCCAA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 9 
               
               
                   
               
               
                 tmDNA Sequence for  Corynebacterium xerosis   
               
               
                 (gram +, high G-C content) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 17) 
               
               
                 GGGGCTGATTCTGGATTCGACTTCGTACATTGAGCCAGGGGAAGCGTGCC 
               
               
                 GGTGAAGGCTGGAGACCACCGCAAGCGTCGCAGCAACCAATTAAGCGCCG 
               
               
                 AGAACTCTCAGCGCGACTACGCCCTCGCTGCCTAAGCAGCGACCGCGTGT 
               
               
                 CTGTCAGACCGGGTAGGCCTCTGATCCGGACCCTGGCATCGTTTAGTGGG 
               
               
                 GCTCGCTCGCCGACTTGGTCGCAAGGGTCGGCGGGGACACTCACTTGCGA 
               
               
                 CTGGGCCCGTCATCCGGTCATGTTCGACTGAACCGGAGGGCCGAGCAGAG 
               
               
                 ACCACGCGCGAACTGCGCACGGAGAAGCCCTGGCGAGGTGACGGAGGACC 
               
               
                 CGGGTTCAACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 10 
               
               
                   
               
               
                 tmDNA Sequence for  Micrococcus luteus  (parfait) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 18) 
               
               
                 GGGGCTATTCTGGATTCGACGGTGTGTGTCGCGTCGGGAGAAGCGGGCCG 
               
               
                 AGGATGCAGAGTCATCTCGTCAAACGCTCTCTGCAAACCAATAAGTGCCG 
               
               
                 AATCCAAGCGCACTGACTTCGCTCTCGCTGCCTGATCAGTGATCGAGTCC 
               
               
                 GTCACCCCGAGGTCGCTGTCGCCTCGGATCGTGGCGTCAGCTAGATAGCC 
               
               
                 ACTGGGCGTCACCCTCGCCGGGGGTCGTGACGCCGACATCAATCCGGCTG 
               
               
                 GGTCCGGGTTGGCCGCCCGTCTGCGGGACGGCCAGGACCGAGCAACACCC 
               
               
                 ACAGCAGACTGCGCCCGGAGAAGACCTGGCAACACCTCATCGGACGCGGG 
               
               
                 TTCAACTCCCGCANTCCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 11 
               
               
                   
               
               
                 tmDNA Sequence for  Mycobacterium smegmatis   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 19) 
               
               
                 TCATCTCGGCTTGTTCGCGTGACCGGGAGATCCGAGTAGAGACATAGCGA 
               
               
                 ACTGCGCACGGAGAGGGGCTGATTCCTGGATTCGACTTCGAGCATCGAAT 
               
               
                 CCAGGGAAGCGTGCCGGTGCAGGCAAGAGACCACCGTAAGCGTCGTTGCA 
               
               
                 ACCAATTAAGCGCCGATTCCAATCAGCGCGACTACGCCCTCGCTGCCTAA 
               
               
                 GCGACGGCTGGTCTGTCAGACCGGGAGTGCCCTCGGCCCGGATCCTGGCA 
               
               
                 TCAGCTAGAGGGACCCACCCACGGGTTCGGTCGCGGGACCTGTGGGGACA 
               
               
                 TCAAACAGCGACTGGGATCGAGCCTCGAGGACATGCCGTAGGACCCGGGT 
               
               
                 TCAACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 12 
               
               
                   
               
               
                 tmDNA Sequence for  Bacillus badius   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 20) 
               
               
                 GGGGGTGATTCTGGATTCGACAGGGATAGTTCGAGCTTGGGCTGCGAGCC 
               
               
                 GGAGGGCCGTCTTCGTACCAACGCAAACGCCTAAATATAACTGGCAAAAA 
               
               
                 AGATTTAGCTTTAGCTGCCTAATATAGGTTCAGCTGCTCCTCCCGCTATC 
               
               
                 GTCCATGTAGTCGGGTAAGGGGTCCAAACTTAGTGGACTACGCCGGAGTT 
               
               
                 CTCCGCCTGGGGACAAAGGAAGAGATCAATCAGGCTAGCTGCCCGGACGC 
               
               
                 CCGTCGATAGGCAAAAGGAACAGTGAACCCCAAATATATCGACTACGCTC 
               
               
                 GTAGACGTTCAAGTGGCGTTATCTTTGGACGTGGGTTCAACTCCCGCCAG 
               
               
                 CTCCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 13 
               
               
                   
               
               
                 tmDNA Sequence for  Bacillus brevis   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 21) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGATGGTAGAGCATGAGAAGCGAGCCGG 
               
               
                 GGGGTTGCGGACCTCGTCACCAACGCAAACGCCATTAACTGGCAACAAAC 
               
               
                 AACTTTCTCTCGCTGCTTAATAACCAGTGAGGCTCTCCCACTGCATCGGC 
               
               
                 CCGTGTGCCGTGGATAGGGCTCAACTTTAACGGGCTACGCCGGAGGCTTC 
               
               
                 CGCCTGGAGCCAAAGGAAGAAGACCAATCAGGCTAGGTGCCAGGTCAGCG 
               
               
                 CGTCACTCCGCGAATCTGTCACCGAAACTCTAAACGAGTGACTGCGCTCG 
               
               
                 GAGATGCTCATGTATCGCTGTTTTCGGACGGGGGTTCGATTCCCGCCGCC 
               
               
                 TCACCCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 14 
               
               
                   
               
               
                 tmDNA Sequence for  Bacillus thermoleovorans   
               
               
                 (50-60 degres) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 22) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGGTAGGTCGAGCTTAAGCGGCGAGCCG 
               
               
                 AGGGGGACGTCCTCGTAAAAACGTCACCTAAAGATAACTGGCAAACAAAA 
               
               
                 CTACGCTTTAGCTGCCTAATTGCTGCAGCTAGCTCCTCCCGCCATCGCCC 
               
               
                 GCGTGGCGTTCGAGGGGCTCATATGGAGCGGGCTACGCCCAAATCCGCCG 
               
               
                 CCTGAGGATGAGGGAAGAGACGAATCAGGCTAGCCGCCGGGAGGCCTGTC 
               
               
                 GGTAGGCGGAACGGACGGCGAAGCGAAATATACCGACTACGCTCGTAGAT 
               
               
                 GCTTAAGTGGCGATGCCTCTGGACGTGGGTTCGATTCCCGCCGCCTCCCC 
               
               
                 ACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 15 
               
               
                   
               
               
                 tmDNA Sequence for  Clostridium innocuum   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 23) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGATATGTCTGGTACAGACTGCAGTCGA 
               
               
                 GTGGTTACGTAATAACCAATTAAATTTAAACGGAAAAACTAAATTAGCTA 
               
               
                 ACCTCTTTGGTGGAAACCAGAGAATGGCTTTCGCTGCTTAATAACCGATA 
               
               
                 TAGGTTCGCAGCCGCCTCTGCATGCTTCTTCCTTGACCATGTGGATGTGC 
               
               
                 GCGTAAGACGCAAGGGATAAGGAATCTGGTTTGCCTGAGATCAGATTCAC 
               
               
                 GAAAATTCTTCAGGCACATTCATCAGCGGATGTTCATGACCTGCTGATGT 
               
               
                 CTTAATCTTCATGGACTAAACTGTAGAGGTCTGTACGTGGGGCTGTTTCT 
               
               
                 GGACAGGAGTTCGATTCCCGCCGCCTCACCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 16 
               
               
                   
               
               
                 tmDNA Sequence for  Clostridium lentocellum   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 24) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGGTCACATCTACTGGGGCAGCCATCCG 
               
               
                 TAGAACGCCGGAGTCTACGTTAAAAGCTGGCACTTAAAGTAAACGCTGAA 
               
               
                 GATAATTTAGCAATCGCTGCCTAATTAAGGCGCAGTCCTCCTAGGTCTTC 
               
               
                 CGCAGCCTAGATCAGGGCTTCGACTCGCGGATCCTTCACCTGGCAAAGCT 
               
               
                 TTGAGCCAACGTGAACACTATGAAGCTACTAAAATCTAGAGCCTGTCTTT 
               
               
                 GGGCGCTAGATGGAGGGAATGTCAAAACAAAGAATATGATGGTAGAGACC 
               
               
                 ACGCTATATGGGCTTTCGGACAGGGGTTCGATTCCCGCCGCCTTCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 17 
               
               
                   
               
               
                 tmDNA Sequence for  Clostridium perfringens   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 25) 
               
               
                 GGGGCTGATTCTGGATTCGACGGGGGTAAGATGGGTTTGATAAGCGAGTC 
               
               
                 GAGGGAAGCATGGTGCCTCGATAATAAAGTATGCATTAAAGATAAACGCA 
               
               
                 GAAGATAATTTTGCATTAGCAGCTTAATTTAGCGCTGCTCATCCTTCCTC 
               
               
                 AATTGCCCACGGTTGAGAGTAAGGGTGTCATTTAAAAGTGGGGAACCGAG 
               
               
                 CCTAGCAAAGCTTTGAGCTAGGAACGGAATTTATGAAGCTTACCAAAGAG 
               
               
                 GAAGTTTGTCTGTGGACGTTCTCTGAGGGAATTTTAAAACACAAGACTAC 
               
               
                 ACTCGTAGAAAGTCTTACTGGTCTGCTTTCGGACACGGGTTCAACTCCCG 
               
               
                 CCACTCCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 18 
               
               
                   
               
               
                 tmDNA Sequence for  Clostridium stercorarium   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 26) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGTTATTGAAGCAAGAGTAGCGGGTAGA 
               
               
                 GGATTCTCGTTGGCCTCTTTAAAAAACGAGAGCTAAAAATAAACGCAAAC 
               
               
                 AACGATAACTACGCTTTAGCTGCTGCGTAAGTAACACGCAGCCCGTCGGC 
               
               
                 CCCGGGGTTCCTGCGCCTCGGGATACCGGCGTCATCAAGGCAGGGAACCA 
               
               
                 GCCGGATCAGGCTTCAGGTCCGGTGGGATTTAATGAAGCTACCGACTTAT 
               
               
                 AAAGCCTGTCTCTGGGCGTTATAAGAAGGGAATGTCAAAACAGAGACTGC 
               
               
                 ACCCGGAGAAGCTCTTGTGGATATGGTTCCGGACACGAGTTCGATTCCCG 
               
               
                 CCGCCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 19 
               
               
                   
               
               
                 tmDNA Sequence for  Enterococcus faecium  (sp.) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 27) 
               
               
                 GGGGCTGATTATGGATTCGACAGGATNGTTGAGCTTGAATTGCGTTTCGT 
               
               
                 AGGTTACGGCTACGTTAAAACGTTACAGTTAAATATAACTGCTAAAAACG 
               
               
                 AAAACAATTCTTTCGCTTTAGCTGCCTAAAAACCAGCTAGCGAAGATCCT 
               
               
                 CCCGGCATCGCCCATGTGCTCGGGTCAGGGTCCTAATCGAAGTGGGATAC 
               
               
                 GCTAAATTTTTCCGTCTGTAAAATTTAGAGGAGCTTACCAGACTAGCAAT 
               
               
                 ACAAGAATGCCTGTCACTCGGCACGCTGTAAAGCGAACCTTTAAATGAGT 
               
               
                 GTCTATGAACGTAGAGATTTAAGTGGGAATATGTTTTGGACGCGGGTTCA 
               
               
                 ACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 20 
               
               
                   
               
               
                 tmDNA Sequence for  Heliobacillus mobilis   
               
               
                 (photosyn/gram +) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 28) 
               
               
                 GGGGCTGATTCTGGATTCGACGGGGAACGTGTTTGCTTGGGATGCGAGCC 
               
               
                 GGGTTGCCGCCAGGACCGTAAAAAGGGCGGAAGGCTTTAATTGCCGAAGA 
               
               
                 TAACTACGCTTTAGCTGCTTAATTGCAGTCTAACCTCTTCTCCTCTGTGC 
               
               
                 TCTCGGTGAGGATGTAAGGGGTCATTTAAGAGAGCTGGCTTCGACCAATT 
               
               
                 CTCGGAGGTCCAAGCGAGATTTATCGAGATAGCCTGACCAACGCTCTGTC 
               
               
                 TGCCGTGCGGAAGGAAGGCGAAATCTAAAACGACAGACTACGCTCGTAGT 
               
               
                 GTCCTTTGTGGGCATTTCTTCGGACGCGGGTTCAACTCCCGCCAGCTCCA 
               
               
                 CCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 21 
               
               
                   
               
               
                 tmDNA Sequence for  Heliospirillum gestii   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 29) 
               
               
                 GGGGCTGATTCTGGATTCGACGGGGAACGTGTTTGCTTAGGACGCGAGCC 
               
               
                 GGGTTGCCGCCAGGACCGTAAAAAGGGCGGAAGGCTTTAATTGCCGAAGA 
               
               
                 TAACTACGCTTTAGCTGCTTAATTGCAGTCTAACCTCTTCTCCTCTGTGC 
               
               
                 TCTCGGTGAGGATGTAAGGGGTCATTTAAGAGAGCTGGCTCGAACCAATT 
               
               
                 CTCGGAGGTTCGGGTAAGACTTATCGAGATAGCCTGACCAACGCTCTGTC 
               
               
                 TGCCGTGCGGAAGGATGGCGAAATCTAAAACGACAGAATACGCTCGTAGT 
               
               
                 GTCCTTTGTGGGCATTTCTTCGGACGCGGGTTCAACTCCCGCCAGCTCCA 
               
               
                 CCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 22 
               
               
                   
               
               
                 tmDNA Sequence for  Lactobacillus acidophilus   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 30) 
               
               
                 GGGGCTGATTCTGGATTCGACAGGCGTAGACCCGCATTGACTGCGGTTCG 
               
               
                 TAGGTTACGTCTACGTAAAAACGTTACAGTTAAATATAACTGCAAATAAC 
               
               
                 AAAAATTCTTACGCATTAGCTGCTTAATTTAGCGCATGCGTTGCTCTTTG 
               
               
                 TCGGTTTACTCGTGGCTGACACTGAGTATCAACTTAGCGAGTTACGTTTA 
               
               
                 ACTACCTCACCTGAATAGTTGAAAAGAGTCTTAGCAGGTTAGCTAGTCCA 
               
               
                 TACTAGCCCTGTTATATGGCGTTTTGGACTAGTGAAGTTCAAGTAATATA 
               
               
                 ACTATGATCGTAGAGGTCAGTGACGAGATGCGTTTGGACAGCGGGTTCAA 
               
               
                 CTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 23 
               
               
                   
               
               
                 tmDNA Sequence for  Staphylococcus epidermidis   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 31) 
               
               
                 GGGGCTGATTCTGCATTCGACAGGGGTCCCCGAGCTTATTAAGCGTGTGG 
               
               
                 AGGGTTGGCTCCGTCATCAACACATTTCGGTTAAATATAACTGACAAATC 
               
               
                 AAACAATAATTTCGCAGTAGCTGCGTAATAGCCACTGCATCGCCTAACAG 
               
               
                 CATCTCCTACGTGCTGTTAACGCGATTCAACCCTAGTAGGATATGCTAAA 
               
               
                 CACTGCCGCTTGAAGTCTGTTTAGATGAAATATAATCAAGCTAGTATCAT 
               
               
                 GTTGGTTGTTTATTGCTTAGCATGATGCGAAAATTATCAATAAACTACAC 
               
               
                 ACGTAGAAAGATTTGTATCAGGACCTCTGGACGCGGGTTCAACTCCCGCC 
               
               
                 AGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 24 
               
               
                   
               
               
                 tmDNA Sequence for  Streptococcus faecium   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 32) 
               
               
                 GGGGCTGATTCTGGATTCGACAGGCACAGTTTGAGCTTGAATTGCGTTTC 
               
               
                 GTAGGTTACGTCTACGTTAAAACGTTACAGTTAAATATAACTGCTAAAAA 
               
               
                 CGAAAACAACTCTTACGCTTTAGCTGCCTAAAAACAGTTAGCGTAGATCC 
               
               
                 TCTCGGCATCGCCCATGTGCTCGAGTAAGGGTCTCAAATTTAGTGGGATA 
               
               
                 CGTGACAACTTTCCGTCTGTAAGTTGTTAAAGAGATCATCAGACTAGCGA 
               
               
                 TACAGAATGCCTGTCACTCGGCAAGCTGTAAAGCGAAACCACAAATGAGT 
               
               
                 TGACTATGAACGTAGATTTTTAAGTGGCGATGTGTTTGGACGCGGGTTCA 
               
               
                 ACTCCCGCCGTTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 25 
               
               
                   
               
               
                 tmDNA Sequence for  Thermoanaerobacterium   
               
               
                   saccharolyticum  ( Bacillus / clostridium ) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 33) 
               
               
                 GGGGTAGTAGAGGTAAAAGTAGCGAGCCGAGGTTCCATCTGCTCGTAAAA 
               
               
                 CGGTGGACTTAAATATAAACGCAAACGATAATTTAGCTTACGCTGCTTAA 
               
               
                 TTACAAGCAGCCGTTCAACCTTTGATTCCCACATCAAAGGATTGGGCGTC 
               
               
                 GATTTAGTGGGGAACTGATTTATCAAAGCTTTGAGATAAATCGGATTTTA 
               
               
                 TGAAGCTACCAAAGCAGTTATCCTGTCACTGGGAGAACTGCAGAGGGAAT 
               
               
                 GTCAAAACAGTGACTGCGCTCGGAGAAGCTTTTACTGTGACACCTTCGGA 
               
               
                 CCGGGGTTCAACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 26 
               
               
                   
               
               
                 tmDNA Sequence for  Mycoplasma fermentans   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 34) 
               
               
                 GGGGCTGATTCTGGATTCGACATGCATTGGGTGATACTAATATCAGTAGT 
               
               
                 TTGGCAGACTATAATGCATCTAGGCTTTATAATCGCAGAAGATAAAAAAG 
               
               
                 CAGAAGAAGTTAATATTTCTTCACTTATGATTGCACAAAAAATGCAATCA 
               
               
                 CAATCAAACCTTGCTTTCGCTTAGTTAAAAGTGACAAGTGGTTTTAAAGT 
               
               
                 TGACATTTTCCTATATATTTTAAAATCGGCTTTTAAGGAGAACAGGAGTC 
               
               
                 TGAAAGGGTTCCAAAAATCTATATTGTTTGCATTTCGGTAGTATAGATTA 
               
               
                 ATTAGAAATGATAAACTGTAAAAAGTATTGGTATTGACTTGGTGTGTGGA 
               
               
                 CTCGGGTTCAACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 27 
               
               
                   
               
               
                 tmDNA Sequence for  Mycoplasma hyorhinis   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 35) 
               
               
                 GGGGCTGATTCTGGATTCGACATACATAAAAGGATATAAATTGCAGTGGT 
               
               
                 CTTGTAAACCATAAGACAATTTCTTTACTAAGCGGAAAAGAAAACAAAAA 
               
               
                 AGAAGATTATTCATTATTAATGAATGCTTCAACTCAATCAAATCTAGCTT 
               
               
                 TTGCATTTTAAAAAACTAGTAGACCAATTTGCTTCTCACGAATTGTAATC 
               
               
                 TTTATATTAGAGAATAGTTAAAAATCTGATCACTTTTTAATGAATTTATA 
               
               
                 GATCACAGGCTTTTTTAATCTTTTTGTTATTTTAGATAAAGAGTCTTCTT 
               
               
                 AAAAATAACTAAACTGTAGGAATTTATATTTAATTATGCGTGGACCCGGG 
               
               
                 TTCAACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 28 
               
               
                   
               
               
                 tmDNA Sequence for  Mycoplasma pirum   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 36) 
               
               
                 GGGGAGTCATGGTTTTGACATGAATGATGGACCCATAGAGGCAGTGGGGT 
               
               
                 ATGCCCCTTATAGCTCAAGGTTTAAATTAACCGACAAAACTGACGAAAAC 
               
               
                 GTTGCCGTTGATACAAATTTATTAATCAACCAACAAGCTCAATTTAACTA 
               
               
                 CGCATTTGCATAGTATAAAAAAATAAATTGTGCTACTCATTGTAATTAGG 
               
               
                 TTACTAAATTACTTTGTTTTATATAGTCCTGTAACTAGTTCTAGTGATGT 
               
               
                 CTATAAACTAGAATGAGATTTATAGACTTATTTGTTGGCGGTTGTGCCAT 
               
               
                 AGCCTAAATCAACAAAGACAATTTATTTATGGTACTAAACTGTAGATTCT 
               
               
                 ATGATGAAATTATTTGTGGAAACGGGTTCGATTCCCGCCATCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 29 
               
               
                   
               
               
                 tmDNA Sequence for  Mycoplasma salivarium   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 37) 
               
               
                 GGGGCTGATTCTGGATTCGACAGGCATTCGATTCATTATGTTGCAGTGGT 
               
               
                 TTGCAAACCATAAGGCACTAGGCTTTTTTAAACGCAAAAGACCAAAAAAC 
               
               
                 AGAAGATCAAGCAGTTGATCTAGCATTTATGAATAATTCACAAATGCAAT 
               
               
                 CAAATCTAGTTTTCGCTTAGTAAAATTAGTCAATTTATTATGGTGCTCAA 
               
               
                 CATAATAAATGGTAGTATGAGCTTAATATCATATGATTTTAGTTAATATG 
               
               
                 ATAGGATTTGTAACTAAACTATGTTATAGAAATTTGTAAATTATATATAT 
               
               
                 GACATAGGAAATTTAATTTACTAAACTGTAGATGCATAATGTTGAAGATG 
               
               
                 TGTGGACCGGGGTTCAACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 30 
               
               
                   
               
               
                 tmDNA Sequence for  Herpetosiphon aurantiacus   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 38) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGAGGGCCAATCGTAAGTGGCAAGCCGA 
               
               
                 GACGCTGAGCCTCGTTAAATCGGCAACGCCATTAACTGGCAAAAACACTT 
               
               
                 TCCGCGCTCCTGTAGCGCTTGCTGCCTAATTAAGGCAACACGTCTCTACT 
               
               
                 AGCCTCAGCCCGATGGGCTTGTAGCGGCGACACTTAGTCGGGTCGCTCCC 
               
               
                 CTAGTTATGTCTGTGGGCTAGGGGCTAAGATTAACAGGCTGGTCGTGGCC 
               
               
                 CGCTTTGTCTATCGGGTGGTGCACCGATAAGATTTAATCAATAGACTACG 
               
               
                 CTTGTAGATGCTTGCGGTTTAACTTTTTGGACGCGGGTTCGATTCCCGCC 
               
               
                 GCCTCACCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 31 
               
               
                   
               
               
                 tmDNA Sequence for  Thermomicrobium roseum   
               
               
                 (352 nts, temp. 70 degrees, green non sulfur) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 39) 
               
               
                 GGGGCTGATTCTGGATTCGACAGGGCCGTAGGTGCGAGGATTGCAGGTCG 
               
               
                 AGGTCGCCCACGGACTCGTAAAAAGGGGCAGCCAAGTAACTGGCGAGCGC 
               
               
                 GAACTCGCTCTGGCTGCGTAATTCACGCAGCCACGTCTGCCCGGACCCTT 
               
               
                 CCCTGGTGGGTTCGGAGCGGGCGCCGCAAGACCGGGGTGCCCCTGGCCCA 
               
               
                 AGCGCCGGTGCGGGCCAGGTCAAGCGTGATCCGGCTCGGCTGACCGGGAT 
               
               
                 CCTGTCGGTGGGAGCCTGGCAGCGACAGTAGAACACCGACTAAGCCTGTA 
               
               
                 GCATATCCTCGGCTGAACGCTCTGGACGCGGGTTCAACTCCCGCCAGCTC 
               
               
                 CACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 32 
               
               
                   
               
               
                 tmDNA Sequence for  Chlorobium limicola   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 40) 
               
               
                 GGGGCTGATTCTGGATTCGACAGGATACGTGTGAGATGTCGTTGCACTCC 
               
               
                 GAGTTTCAGCATGGACGGACTCGTTAAACAAGTCTATGTACCATTAGATG 
               
               
                 CAGACGATTATTCGTATGCAATGGCTGCCTGATTAGCACAAGTTAACTCA 
               
               
                 GACGCCATCGTCCTGCGGTGAATGCGCTTACTCTGAAGCCGCCGGATGGC 
               
               
                 ATAACCCGCGCTTGAGCCTACGGGTTCGCGCAAGTAAGCTCCGTACATTC 
               
               
                 ATGCCCGAGGGGCTGTGCGGGTAATTTCTCGGGATAAGGGGACGAACGCT 
               
               
                 GCTGGCGGTGTAATCGGCCCACGAAAACCCAATCACCAGAGATGAGTGTG 
               
               
                 GTGACTGCATCGAGCAGTGTTTTGGACGCGGGTTCAACTCCCGCCAGCTC 
               
               
                 CACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 33 
               
               
                   
               
               
                 tmDNA Sequence for  Pirellula staleyi   
               
               
                 ( planctomyces ) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 41) 
               
               
                 GGGGCTGATTCTGGATTCGACCGGATAGCCTGAAGCGAATACGGCGTGCC 
               
               
                 GTGGTTGATCAGATGGCCACGTAAAAAGCTGATCACAAACTTAACTGCCG 
               
               
                 AGAGCAATCTCGCACTTGCTGCCTAACTAAACGGTAGCTTCCGACTGAGG 
               
               
                 GCTTTAGCCGGAGAGGCCCAAAAGTTGGTCACCAAATCCGGACCGCCTCG 
               
               
                 TGCCATGATCGAAACGCACGAGGTCAAAAAAGTTTCGATCTAGTGCAGGG 
               
               
                 TGTAGCCAGCAGCTAGGCGACAAACTGTGCAAAAATCAAATTTTCTGCTA 
               
               
                 CGCACGTAGATGTGTTCGTGAAAATGTCTCGGGACGGGGGTTCAACTCCC 
               
               
                 GCCACTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 34 
               
               
                   
               
               
                 tmDNA Sequence for  Planctomyces limnophilus   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 42) 
               
               
                 GGGGCTGATTCTGGATTCGACAACCTCTCAAGAGGAGCGTGGCCACTATG 
               
               
                 GGACTCGATTATGTTGAATTCGTCATGGATCTTGAAGAGACCTTCGACAT 
               
               
                 CAAACTGGATGACAAACATTTTTCAGCAGTCAAAACACCACGCGATTTGG 
               
               
                 CAATCATTATTCGGGATCAATTAGCTGCTGAAGGCAGAATCTGGGATGAA 
               
               
                 TCGAATGCTTTTCGCAAAATCTCGAATTTGAATTGGACGATGTTGCCCGA 
               
               
                 GTTCCGGATGTGGACTCAAATCAAAAGCTCTCTACCAGTTTCTTTTCACC 
               
               
                 GACTGCGTCCCAGCACCCGTCTCGTTCAACTCCCGCCANTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 35 
               
               
                   
               
               
                 tmDNA Sequence for  Planctomyces maris   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 43) 
               
               
                 GGGGCTGATTCTGGATTCGACTGGTTCACCGTATGTTAAGGTGGCGGTGC 
               
               
                 CGTGGTTGATCAGTTGGCCACGTAAAAAGCTGATCACAATCTAATTGCAA 
               
               
                 ACAAGCAATTTTCAATGGCTGCTTAATAAAAGCAACCCCGGCTTAGGAAT 
               
               
                 CTCTGTCTGAGGAGTCCGACAGCTGGTCACAAAATCAGACTGGTATCAGA 
               
               
                 TCAATGTCCGCTCCGTCTGATACGAGATTCGTGGTGGACTGGTTTCCAAC 
               
               
                 AGGCTCTGTTTATCGTGCCCGAAGAAACGAGACTCAAACGATAAAATATG 
               
               
                 CACCGTAGAGGCTTTAGCTGAGGGTTCACAGGACGCGGGTTCAACTCCCG 
               
               
                 CCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 36 
               
               
                   
               
               
                 tmDNA Sequence for  Alcaligenes eutrophus   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 44) 
               
               
                 GGGGTTGATTCTGGATTCGACGTGGGTTACAAAGCAGTGGAGGGCATACC 
               
               
                 GAGGACCCGTCACCTCGTTAATCAATGGGAATGCAATAACTGCTAACGAC 
               
               
                 GAACGTTACGCACTGGCCGCTTAATTGCGGCCGTCCTCGCACTGGCTCGC 
               
               
                 TGACGGGCTAGGGTCGCAAGACCACGCGAGGTCATTTACGTCAGATAAGC 
               
               
                 TCCGGAAGGGTCACGAAGCCGGGGACGAAAACCTAGTGACTCGCCGTCGT 
               
               
                 AGAGCGTGTTCGTCCGCGATGCGCCGGTTAAATCAAATGACAGAACTAAG 
               
               
                 TATGTAGAACTCTCTGTGGAGGGCTTACGGACGCGGGTTCAACTCCCGCC 
               
               
                 AGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 37 
               
               
                   
               
               
                 tmDNA Sequence for  Alcaligenes faecalis   
               
               
                 (beta proteobacteria) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 45) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGGTCAAGAAGCAGCACAGGGCGTGTCG 
               
               
                 AGCACCAGTACGCTCGTAAATCCACTGGAAAACTATAAACGCCAACGACG 
               
               
                 AGCGTTTCGCTCTAGCCGCTTAAGGCTGGGCCACTGCACTAATTTGTCTT 
               
               
                 TGGGTTAGGTAGGGCAACCTACAGCAGTGTTATTTACAAAGAATCGAATC 
               
               
                 GGTCTGCGCCACGAAGTCCGGTTCTAAAACTTAGTGGATCGCCAAGGAAA 
               
               
                 GGCCTGTCAATTGGCATAGTCCAAGGTTAAAACTTAAAATTAATTGACTA 
               
               
                 CACATGTAGAACTGTCTGTGGACGGCTTGCGGACGGGGGTTCGATTCCCG 
               
               
                 CCGCCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 38 
               
               
                   
               
               
                 tmDNA Sequence for  Chromobacterium violaceum   
               
               
                 (beta-purple) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 46) 
               
               
                 GGGGCTGATTCTGGATTCGACGGGGGTTGCGAAGCAGATGAGGGCATACC 
               
               
                 GGGATTTCAGTCACCCCGTAAAACGCTGAATTTATATAGTCGCAAACGAC 
               
               
                 GAAACTTACGCTCTGGCAGCCTAACGGCCGGCCAGACACTACAACGGTTC 
               
               
                 GCAGATGGGCCGGGGGCGTCAAAACCCTGTAGTGTCACTCTACATCTGCT 
               
               
                 AGTGCTGTTCCGGGTTACTTGGTTCAGTGCGAAATAATAGGTAACTCGCC 
               
               
                 AAAGTCCAGCCTGTCCGTCGGCGTGGCAGAGGTTAAATCCAAATGACACG 
               
               
                 ACTAAGTATGTAGAACTCACTGTAGAGGACTTTCGGACGCGGGTTCAACT 
               
               
                 CCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 39 
               
               
                   
               
               
                 tmDNA Sequence for  Hydrogenophaga palleroni   
               
               
                 (beta-purple) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 47) 
               
               
                 GGGGCTGATTCTGGATTCGACGTGGGTTCGGACGCGCAGCAGGGCATGTC 
               
               
                 GAGGTTCTGTCACCTCGTAAATCAGCAGAAAAAAACCAACTGCAAACGAC 
               
               
                 GAACGTTTCGCACTCGCCGCTTAAACACCGGTGAGCCTTGCAACAGCAGG 
               
               
                 CCGATGGGCTGGGCAAGGGGGTCGCAAGACCTCCCGGCTGCAAGGTAATT 
               
               
                 TACATCGGCTGGTTCTGCGTCGGGCACCTTGGCGCAGGATGAGATTCAAG 
               
               
                 GATGCTGGCTTCCCGTTTAGCGTGCCACTGCGCGACTCGGGCGGCGAGAC 
               
               
                 CCAAATCAGACGGCTACACATGTAGAACTGCTCGAAAAAGGCTTGCGGAC 
               
               
                 GGGGGTTCAACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 40 
               
               
                   
               
               
                 tmDNA Sequence for  Methylobacillus glycogenes   
               
               
                 (beta-purple) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 48) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGGTTGCAAAGCAGCGCAGGGCATACCG 
               
               
                 AGGCCTAGTCACCTCGTAAATAAACTAGAACAAGTATAGTCGCAAACGAC 
               
               
                 GAAACTTACGCTCTAGCCGCTTAATCCCGGCTGGACGCTGCACCGAAGGG 
               
               
                 CCTCTCGGTCGGGTGGGGTAACCCACAGCAGCGTCATTAAGAGAGGATCG 
               
               
                 TGCGATATTGGGTTACTTAATATCGTATTAAATCCAAGGTAACTCGCCTG 
               
               
                 CTGTTTGCTTGCTCGTTGGTGAGCATCAGGTTAAATCAAACAACACAGCT 
               
               
                 AAGTATGTAGAACTGTCTGTGGAGGGCTTGCGGACGGGGGTTCGATTCCC 
               
               
                 GCCGCCTCACCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 41 
               
               
                   
               
               
                 tmDNA Sequence for  Nitrosomonas cryotolerans   
               
               
                 (beta-purple) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 49) 
               
               
                 GGGGCTGATTCTGGATTCGACGTGGGTTGCAAAGCAGCGCAGGGCATACC 
               
               
                 GAGGACCAGAATACCTCGTAAATACATCTGGAAAAAAATAGTCGCAAACG 
               
               
                 ACGAAAACTACGCTTTAGCCGCTTAATACGGCTAGCCTCTGCACCGATGG 
               
               
                 GCCTTAACGTCGGGTCTGGCAACAGACAGCAGAGTCATTAGCAAGGATCG 
               
               
                 CGTTCTGTAGGGTCACTTTACAGAACGTTAAACAATAGGTGACTCGCCTG 
               
               
                 CCATCAGCCCGCCAGCTGGCGGTTGTCAGGTTAAATTAAAGAGCATGGCT 
               
               
                 AAGTATGTAGAACTGTCTGTAGAGGACTTGCGGACGCGGGTTCAACTCCC 
               
               
                 GCCAGTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 42 
               
               
                   
               
               
                 tmDNA Sequence for  Pseudomonas testosteroni   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 50) 
               
               
                 GGGGCTGATTCTGGATTCGACGTGGGTTCGGGACCGGTGCGGTGCATGTC 
               
               
                 GAGCTTGAGTGACGCTCGTAAATCTCCATTCAAAAAACTAACTGCAAACG 
               
               
                 ACGAACGTTTCGCACTCGCCGCTTAATCCGGTGAGCCTTGCAACAGCACG 
               
               
                 CTAGTGGGCTGGGCAAGGGGGTAGCAATACCTCCCGGCTGCAAGGGAATT 
               
               
                 TTCATTAGCTGGCTGGATACCGGGCTTCTTGGTATTTGGCGAGATTTTAG 
               
               
                 GAAGCTGGCTACCCAAGCAGCGTGTGCCTGCGGGGTTTGGGTGGCGAGAT 
               
               
                 TTAAAACAGAGCACTAAACATGTAGATCTGTCCGGCGAAGGCTTACGGAC 
               
               
                 GCGGGTTCAACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 43 
               
               
                   
               
               
                 tmDNA Sequence for  Ralstonia pickettii   
               
               
                 ( Burkholderia ) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 51) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGGTTGCGAAGCAGCGGAGGGCATACCG 
               
               
                 AGGACCCGTCACCTCGTTAATCAATGGGAATGCAATAACTGCTAACGACG 
               
               
                 AACGTTACGCACTGGCAGCCTAAGGGCCGCCGTCCTCGCACTGGCTCGCT 
               
               
                 GACGGGCTAGGGTCGCAAGACCAGCGAGGTCATTTACGTCAGATAAGCTT 
               
               
                 TAGGTGAGTCACGGGCCTAGAGACGAAAACTTAGTGAATCGCCGTCGTAG 
               
               
                 AGCGTGTTCGTCCGCGATGCGGCGGTTAAATCAAATGACAGAACTAAGTA 
               
               
                 TGTAGAACTCTCTGTGGAGGGCTTGCGGACGCGGGTTCGATTCCCGCCGC 
               
               
                 CTCACCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 44 
               
               
                   
               
               
                 tmDNA Sequence for  Variovax paradoxus   
               
               
                 ( pseudomonas  sp.) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 52) 
               
               
                 GGGGCTGATTCTGGATTCGACGTGGGTTCGGAGTCGCAGCGGGGCATGTC 
               
               
                 GAGCTGAATGCGCTCGTAAAACAGATTCAAACAAACTAACTGCAAACGAC 
               
               
                 GAACGTTTCGCACTCGCTGCTTAATTGCCAGTGAGCCTTGCAACAGTTGG 
               
               
                 CCGATGGGCTGGGCAAGGGGGTCTGGAGCAATCCTGACCTCCCGGCTGCA 
               
               
                 AGGATAACTACATGGGCTGGCTCCGATCCGGGTACCTTGGGTCGGGGCGA 
               
               
                 GAAAATAGGGTACTGGCGTCCGGTTTAGCGTGTGACTGCGCGACTCCGGA 
               
               
                 AGCGAGACTCAAAACAGATCACTAAACATGTAGAACTGCGCGATGAAGGC 
               
               
                 TTGCGGACGGGGGTTCAACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 45 
               
               
                   
               
               
                 tmDNA Sequence for  Bdellovibrio bacteriovorus   
               
               
                 (delta proteobacterie) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 53) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGGTGCTGAAGCATAAGGAGCATACCGG 
               
               
                 GGCGGATGAGGACCTCGTTAAAAACGTCCACTTTGTAATTGGCAACGATT 
               
               
                 ACGCACTTGCAGCTTAATTAAGCAGCACGATCAACCTTGTGGTGGTTCCG 
               
               
                 CACTTGGATTGATCGTCATTTAGGGACCTCGGCGTGTTGGGTTTTCTCCA 
               
               
                 GCAGACATGCTTAAATTTACTGGGGGAGAGGTCTTAGGGATTTTGTCTGT 
               
               
                 GGAAGCCCGAGGACCAATCTAAAACACTGACTAAGTATGTAGCGCCTTAT 
               
               
                 CGTGGATCATTTGCGGACGGGGGTTCGATTCCCGCCGCCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 46 
               
               
                   
               
               
                 tmDNA Sequence for  Myxococcus xanthus   
               
               
                 (delta proteobacterie) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 54) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGGCATTGAAGTTCGAGACGCGTGCCGA 
               
               
                 GCTTGTCAGGTAGCTCGTAAATTCAACCCGGCAAAGACACAAAAGCCAAC 
               
               
                 GACAACGTTGAGCTCGCGCTGGCTGCCTAAAAACAGCCCATAGTGCGCGG 
               
               
                 TCCCCCCGCCCTCGGCCTGTGGGGTTGGGACAGACCGTCATAATGCAGGC 
               
               
                 TGGCTGCCGAGGGTGCCTGGACCCGAGGTGGCGAGATCTTCCCAGGACCG 
               
               
                 GCTCTGAGTATCCCGTCCGTGGGAGCCTCAGGGACGTAGCAAATCGCGGA 
               
               
                 CTACGCACGTAGGGTCGAAGAGCGGACGGCTTTCGGACGCGGGTTCGATT 
               
               
                 CCCGCCGCCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 47 
               
               
                   
               
               
                 tmDNA Sequence for  Sulfurospirillum Deleyianum   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 55) 
               
               
                 GGGGCTGATTCTGGATTCGACAGGAGTAGTTTTAGCTTATGGCTGCATGT 
               
               
                 CGGGAGTGAGGGTCTTCCGTTACACAACCTTCAAACAATAACTGCTAACA 
               
               
                 ACAGTAACTATCGTCCTGCTTACGCGCTAGCTGCGTAAGTTTAACAAATA 
               
               
                 ATGGACTGCTCTCCCCTTTGATGCTATCTTAGGAGGTCTTGGAGAGTATC 
               
               
                 ATAGATTTGATAGCTATATTACATGAACGCCTTTACATGTAATGAAGTTA 
               
               
                 AAGGCTCGTTTTGCGTAGTTTTCTGATTGTTGTACGAAGCAAAATTAAAC 
               
               
                 ACTATCAACAATATCTAAGCATGTAGACGTCATAGGTGGCTATTTTTGGA 
               
               
                 CTGCGGGTTCAACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 48 
               
               
                   
               
               
                 tmDNA Sequence for  Chromatium vinosum   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 56) 
               
               
                 GGGGCTGATTCTGGATTCGACGTGGGTCGCGAAACCTAAGGTGCATGCCG 
               
               
                 AGGTGCGGTTGACCTCGTAAAACCCTCCGCAAACTTATAGTTGCCAACGA 
               
               
                 CGACAACTACGCTCTCGCTGCTTAATCCCAGCGGGCCTCTGACCGTCACT 
               
               
                 TGCCTGTGGGCGGCGGATTCCAGGGGTAACCTCACACAGGATCGTGGTGA 
               
               
                 CGGGAGTCCGGACCTGATCCACTAAAACCTAACGGAATCGCCGACTGATC 
               
               
                 GCCCTGCCCTTCGGGCGGCAGAAGGCTAAAAACAATAGAGTGGGCTAAGC 
               
               
                 ATGTAGGACCGAGGGCAGAGGGCTTGCGGACGCGGGTTCAACTCCCGCCA 
               
               
                 GCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 49 
               
               
                   
               
               
                 tmDNA Sequence for  Pseudomonas fluorescens   
               
               
                 (gamma proteobacteria) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 57) 
               
               
                 GGGGCTGATTCTGGATTCGACGCCGGTTGCGAACCTTTAGGTGCATGCCG 
               
               
                 AGTTGGTAACAGAACTCGTAAATCCACTGTTGCAACTTTCTATAGTTGCC 
               
               
                 AATGACGAAACCTACGGGGAATACGCTCTCGCTGCGTAAGCAGCCTTAGC 
               
               
                 CCTTCCCTCCTGGTACCTTCGGGTCCAGCAATCATCAGGGGATGTCTGTA 
               
               
                 AACCCAAAGTGATTGTCATATAGAACAGAATCGCCGTGCAGTACGTTGTG 
               
               
                 GACGAAGCGGCTAAAACTTACACAACTCGCCCAAAGCACCCTGCCCGTCG 
               
               
                 GGTCGCTGAGGGTTAACTTAATAGACACGGCTACGCATGTAGTACCGACA 
               
               
                 GCAGAGTACTGGCGGACGCGGGTTCAACTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 50 
               
               
                   
               
               
                 tmDNA Sequence for  Borrelia afzeli   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 58) 
               
               
                 GGGGCTGATTCTGGATTCGACTGAAAATGCTAATATTGTAAGTTGCAAGC 
               
               
                 AGAGGGAATCTCTTAAAACTTCTAAAATAAATGCAAAAAATAATAACTTT 
               
               
                 ACAAGTTCAAACCTTGTAATGGCTGCTTAAGTTAGCAGAGAGTTTTGTTG 
               
               
                 AATTTGGCTTTGAGATTCACTTATACTCTTTTAGACATCGAAGCTTGCTT 
               
               
                 AAAAATGTTTTCAAGTTGATTTTTAGGGACTTTTATACTTGAGAGCAATT 
               
               
                 TGGCGGTTTGCTAGTATTTCCAAACCATATTGCTTAGTAAAATACTAGAT 
               
               
                 AAGCTTGTAGAAGCTTATAGTATTGTTTTTAGGACGCGGGTTCAACTCCC 
               
               
                 GCCAGTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 51 
               
               
                   
               
               
                 tmDNA Sequence for  Borrelia crociduarae   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 59) 
               
               
                 GGGGCTGATTCTGGATTCGACTAAGAACTTTAGTAGCATAAATGGCAAGC 
               
               
                 AGAGTGAATCTCTTAAAACTTCTTTAATAAATGCAAAAAATAATAACTTT 
               
               
                 ACAAGTTCAGATCTTGTAATGGCTGCTTAATTTAGCAGAGAGTTTTGTTG 
               
               
                 GATTTTGCTTTGAGGTTCAACTTATACTCTTTAAGACATCAAAGTATGCC 
               
               
                 TAAAAATGTTTCAAGTTGATTTTTAGGGACCTTTAAACTTGAGAGTAATT 
               
               
                 TGGTGGTTTGCTTGTTTTCCAAGCCTTATTGCTTTTTCTAAAAATTAGCT 
               
               
                 AAGCTTGTAGATATTTATGATATTATTTTTAGGACGCGGGTTCAACTCCC 
               
               
                 GCCAGTTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 52 
               
               
                   
               
               
                 tmDNA Sequence for  Borrelia hermsii   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 60) 
               
               
                 GGGGCTGATTCTGGATTCGACTAAAAACTTTAGTAGCATAAATTGCAAGC 
               
               
                 AGAGGGAATCTCTTAAAACTTCTTTAATAAATGCAAGAAATAATAACTTT 
               
               
                 ACAAGTTCAAATCTTGTAATGGCTGCTTAAATTAGCAGAGAGTTCTGCTG 
               
               
                 GATTTTGCTTTGAGGTTCAGCTTATACTCTTTTAAGACATCAAAGCTTGC 
               
               
                 TTAAAAATATTTCAAGTTGATTTTTAGGGACTTTTAAATTTGAGAGTAAT 
               
               
                 TTGGCGGTTTGCTAGTTTTTCCAAACCTTATTACTTAAAGAAAACACTAG 
               
               
                 CTAAGCTTGTAGATATTTATGATATTATTTTTAGGACGCGGGTTCAACTC 
               
               
                 CCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 53 
               
               
                   
               
               
                 tmDNA Sequence for  Borrelia garinii   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 61) 
               
               
                 GGGGCTGATTCTGGATTCGACTGAAAATGCGAATATTGTAAGTTGCAGGC 
               
               
                 AGAGGGAATCTCTTAAAACTTCTAAAATAAATGCAAAAAATAATAACTTT 
               
               
                 ACAAGCTCAAACCTTGTAATGGCTGCTTAAGTTAGCAGGGAGTTTCGTTG 
               
               
                 AATTTGGCTTTGAGGTTCACTTATACTCTTTTCGATATCGAAGCTTGCTT 
               
               
                 AAAAATGTTTTCAAGTTAATTTTTAGGGACTTTTGTACTTGAGAGCAATT 
               
               
                 TGGCGGTTTGCTAGTATTTCCAAACCATATTGCTTAAGTAAAATGCTAGA 
               
               
                 TAAGCTTGTAGAAGCTTATAATATTGTTTTTAGGACGCGGGTTCAACTCC 
               
               
                 CGCCAGTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 54 
               
               
                   
               
               
                 tmDNA Sequence for  Thermodesulfobacterium commune   
               
               
                 (70 degrees) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 62) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGATAGGTAGGATTAAACAGCAGGCCGT 
               
               
                 GGTCGCACCCAACCACGTTAAATAGGGTGCAAAAACACAACTGCCAACGA 
               
               
                 ATACGCCTACGCTTTGGCAGCCTAAGCGTGCTGCCACGCACCTTTAGACC 
               
               
                 TTGCCTGTGGGTCTAAAGGTGTGTGACCTAACAGGCTTTGGGAGGCTTAA 
               
               
                 TCGGTGGGGTTAAGCCTCCCGAGATTACATCCCACCTGGTAGGGTTGCTT 
               
               
                 GGTGCCTGTGACAAGCACCCTACGAGATTTTCCCACAGGCTAAGCCTGTA 
               
               
                 GCGGTTTAATCTGAACTATCTCCGGACGCGGGTTCGATTCCCGCCGCCTC 
               
               
                 CCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 55 
               
               
                   
               
               
                 tmDNA Sequence for  Thermotoga neapolitana   
               
               
                 ( Thermotogales ) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 63) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGATGGAGTCCCCTGGGAAGCGAGCCGA 
               
               
                 GGTCCCCACCTCCTCGTAAAAAAGGTGGGAACACGAATAAGTGCCAACGA 
               
               
                 ACCTGTTGCTGTTGCCGCCTAATAGATAGGCGGCCGTCCTCTCCGGAGTT 
               
               
                 GGCTGGGCTCCGGAAGAGGGCGTGAGGGATCCAGCCTACCGATCTGGGCT 
               
               
                 CCGCCTTCCGGCCCGGATCGGGAAGGTTCAGGAAGGCTGTGGGAAGCGAC 
               
               
                 ACCCTGCCCGTGGGGGGTCCTTCCCGAGACACGAAACACGGGCTGCGCTC 
               
               
                 GGAGAAGCCCAGGGGCCTCCATCTTCNGACGCGGGTTCGATTCCCGCCAC 
               
               
                 CTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 56 
               
               
                   
               
               
                 tmDNA Sequence for  Deinococcus proteolyticus   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 64) 
               
               
                 GGGGGCGGAAAGGATTCGACGGGGGAACGGAAAGCGCTGCTGCGTGCCGA 
               
               
                 GGAGCCGTTGGCCTCGTAAACAAACGGCAAAGCCATTAACTGGCGAAAAT 
               
               
                 AACTACGCTCTCGCTGCTTAAGTGAGACAGTGACCACGTAGCCCCGCCTT 
               
               
                 TGGCGACGTGTGAACTGAGACAAAAGAAGGCTAGCTTAGGTGAGGTTCCA 
               
               
                 TAGCCAAAAGTGAAACCAAATGGAAATAAGGCGGACGGCAGCCTGTTTGC 
               
               
                 TGGCAGCCCAGGCCCGACAATTTAAGAGCAGACTACGCACGTAGATGCAC 
               
               
                 GCTGGATGGACCTTTGGACGCGGGTTCGATTCCCGCCAGCTCCACCA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 57 
               
               
                   
               
               
                 tmDNA Sequence for  Prosthecobacter fusiformis   
               
               
                 ( verrucomicrobia ) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 65) 
               
               
                 GGGGCTGATTCTGGATTCGACGGGGAGTACAAGGATCAAAAGCTGCAAGC 
               
               
                 CGAGGTGCCGTTACCTCGTAAAACAACGGCAAAAAAGAAGTGCCAACACA 
               
               
                 AATTTAGCATTAGCTGCTTAATTTAGCAGCTACGCTCTTCTAACCCGGGC 
               
               
                 TGGCAGGGTTAGAAGGGTGTCATAATGAGCCAGCTGCCCCTTCCGACTCC 
               
               
                 CCTAAGGAAGGGAAAGATGTAGGGGATAGGTGCTTACAGAATCCTGCGGG 
               
               
                 AGGGAGTCTGTAAGTGCCGAAAAGTTAAAACTCCCGCTAAGCTTGTAGAG 
               
               
                 GCTTTTGATTCTTGCTCTCTGGACGCGGGTTCAACTCCCGCCAGCTCCAC 
               
               
                 CA 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 58 
               
               
                   
               
               
                 tmDNA Sequence for  Verrucomicrobium spinosum   
               
               
                 ( verrucomicrobium ) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
            
               
                 (SEQ ID NO: 66) 
               
               
                 GGGNNNNATTTGGAATTCGCCGAATGCTAGAAGTGGAGGCTGCATGCCGC 
               
               
                 GGATGATTCGTTGGCCGCTTTACCAATTCGGATCAAACAACTAAATGCGG 
               
               
                 ACTCTAACGAGCTTGCCCTCGCCGCTTAATTGACGGTGACGTTCCTCCAG 
               
               
                 TGAAGTCTGTGAATTGGAGGAGCGACTACTTACAGGCTGGCCAAAAGAGC 
               
               
                 GGGCGACCGGCCCCAAGGCGAGATCTACAGGCCGCTGGATGGACGGCATC 
               
               
                 CTGGCAGTAGGAGGCTGGACATCGAGATCAAATNATTGCCTGAGCATGGA 
               
               
                 GACGCTTTCATAAAGGNGTTCGGACAGGG 
               
               
                   
               
            
           
         
       
     
     Example 4 
     Alignment of tmRNA Sequences 
     The newly discovered tmRNA sequences and several known tmRNA sequences were aligned to identify target sites for drug development. The alignments of the sequences are shown in  FIGS. 3A-11B . The nucleotides in the tmRNA sequences of these figures exist in several motifs (Felden et al., 1999). These motifs include nucleotides considered to be in RNA helices (Watson-Crick base-pairs GC or AU, or GU Wobble base-pairs). Nucleotides that are in single stranded RNA domains, hence not base-paired. Some nucleotides in the single stranded domains are universally conserved nucleotides. Other nucleotides are the exceptions to a quasi-sequence conservation in the sequences alignment. Several nucleotides exist in well established non-canonical structural motifs in RNA structures; for example AG-GA pairs, AA pairs, etc. Some nucleotides are universally conserved Wobble GU base-pairs. 
     All the gene sequences have been decomposed in several structural domains that have been indicated with names at the top of each block of sequences. These domains are respectively from the 5′-end to the 3′-end of the sequences: H1, H5, H2, PK1, H4, PK2, PK3, PK4, H5 and H6. The bars delineate all the structural domains. H means helices and PK means pseudoknot. A pseudoknot is made of the pairing of parts of an RNA-loop with an upstream sequence. Consequently, two helices are made (shown in Felden et al., 1999) for all the 4 pseudoknots PK1 to PK4 for each sequence. Moreover, the tRNA-like domain as well as the coding sequence, namely the two functional units of the molecule, have also been indicated for each sequence. 
     The sequences, especially as identified by the sequence alignment, represent targets for the development of drugs which may be broadly applicable to many kinds of bacteria, or may be broadly applicable only to a particular genera of phylum of bacteria, or may be specifically applicable to a single species of bacteria. 
     Common Structural Features for Drug Targeting: 
     For all the novel tmRNA sequences, as well as with the ones that are already known, there are systematically several structural domains that are always found. These domains can be used as targets for the development of drugs which may be genera specific or which may be eubacteria specific. These domains are either RNA helices which can be sometimes interrupted by bulges or pseudoknots. The RNA helices which are always present are H1, H2, H5 and H6. Helices H1 and H6 are found in all canonical transfer RNAs. Thus, H1 and H6 are not good targets for drug development because drugs that would target them will also interfere with the biology of the individual that has a given disease. Consequently, very good candidates for development of drugs for targeting as many bacteria as possible are helices H2 and H5. Moreover, helices H2 and H5 are critical for the folding of all these tmRNA since both of them connect the two ends of the molecule together. Disruption of either H2 or H5 with a specific drug would lead to inactive tmRNA molecules in vivo. Similarly, pseudoknots PK1, PK2 and PK3 are always found in the bacterial tmRNAs. The PK1 structural domain is strictly conserved in the tmRNAs and is located upstream of the coding sequence. Since these pseudoknots are not found in all canonial transfer RNAs, they can also be targeted with specific drugs. Disruption of either PK1 or PK2 or PK3 with a specific drug would lead to inactive tmRNA molecules in vivo. 
     Specific Structural Features in Each Phylum that could be Targeted by Drugs: 
     In addition to developing drugs which broadly target many bacteria, drugs are developed which are more genera specific. For trying to target specifically a given bacteria or a complete phylum, the coding sequence (shown in all the alignments) is a very good candidate. Indeed, this region of the RNA is very accessible for DNA antisense binding, which has been shown for  Escherichia coli , and thus, is also available for interaction with other drugs. Moreover, this is a critical functional domain of the molecule in its quality-control mechanism in cells. In addition, this coding sequence would be the ideal target to use for designing specific PCR-based diagnostic assays for infection diseases. 
     Interestingly, some structural domains are present only in a given bacterial phyla and could be targeted for discovering a drug that will be specific of a phylum, but not of the others. For example: 
     (1) in the cyanobacteria, the fourth pseudoknot PK4 is made of two smaller pseudoknots called PK4a and PK4b; 
     (2) in the mycoplasma, helix H2 is made of only 4 base-pairs instead of 5 in the other species; 
     (3) for two sequences of chlorobium as well as  Bacteroides thetaiotaomicron  and ppm gingiv., there is an additional domain just downstream of the coding sequence that is unique to them; 
     (4) there is always a stem-loop in the coding sequence of the actinobacteria (Felden et al., 1999); and 
     (5) all the beta proteobacteria possess a sequence insertion in pseudoknot PK2 (shown in the alignment). 
     The novel sequences described herein, when aligned, show that specific structural domains within tmRNA are strictly conserved, as for example pseudoknot PK1 is located upstream (at the 5′-side) of the coding sequence. As previously disclosed, this pseudoknot is a target for future anti-bacterial drugs. Moreover, recent data have shown that this PK1 pseudoknot, among all the four pseudoknots within tmRNA gene sequences (sometimes there&#39;s only 2 or 3 detectable pseudoknots, depending upon the sequences), is the only one that its correct folding is essential for the biological activity of tmRNA (Nameki et al., 1999; Nameki et al., 2000). 
     While the invention has been disclosed in this patent application by reference to the details of preferred embodiments of the invention, it is to be understood that the disclosure is intended in an illustrative rather than in a limiting sense, as it is contemplated that modifications will readily occur to those skilled in the art, within the spirit of the invention and the scope of the appended claims. 
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