Controlling bacterial biofilms

Abstract

Methods of controlling bacteria cells are disclosed. These methods comprise upregulating expression of a DVU2956 sigma 54-dependent enhancer-binding protein (EBP) in bacteria cells, resulting in (i) dispersing a biofilm of the cells or reducing biofilm formation by the cells, and/or (ii) reducing hydrogen sulfide formation by the cells. Further disclosed are methods of identifying compounds for controlling bacteria cells as in (i) and/or (ii) above. Polynucleotides and cells are disclosed that can optionally be used to practice compound identification methods.

What is claimed is: 
     
         1 . A method of controlling bacteria cells, said method comprising:
 upregulating expression of a DVU2956 sigma 54-dependent enhancer-binding protein (EBP) in the bacteria cells,   thereby (i) dispersing a biofilm of the cells or reducing biofilm formation by the cells, and/or (ii) reducing hydrogen sulfide formation by the cells.   
     
     
         2 . The method of  claim 1 , wherein the cells are sulfate-reducing bacteria (sulfide-producing bacteria) cells. 
     
     
         3 . The method of  claim 2 , wherein the cells are of the order Desulfovibrionales. 
     
     
         4 . The method of  claim 3 , wherein the cells are of the genus  Desulfovibrio.    
     
     
         5 . The method of  claim 1 , wherein said DVU2956 sigma 54-dependent EBP is endogenous to the cells. 
     
     
         6 . The method of  claim 1 , wherein the cells are comprised within a biofilm, and the biofilm is dispersed following the upregulation step. 
     
     
         7 . The method of  claim 6 , wherein expression of said DVU2956 sigma 54-dependent EBP, prior to the upregulation step, is repressed by the cells. 
     
     
         8 . The method of  claim 1 , wherein the cells are treated with at least one compound to induce the upregulated expression of said DVU2956 sigma 54-dependent EBP. 
     
     
         9 . The method of  claim 1 , wherein the cells are on one or more surfaces of industrial equipment or are otherwise present in an industrial process. 
     
     
         10 . A method of identifying a candidate compound for controlling bacteria cells, said method comprising:
 (a) providing bacteria cells comprising a polynucleotide that comprises (i) a DVU2956 sigma 54-dependent enhancer-binding protein (EBP) regulatory sequence operably linked to (ii) a nucleotide sequence;   (b) contacting the bacteria cells of step (a) with at least one test compound; and   (c) determining whether expression of said nucleotide sequence by the bacteria cells of step (b) is upregulated, wherein such upregulation indicates that the test compound is a candidate compound for (i) controlling biofilm maintenance or biofilm formation by said bacteria cells or other bacteria cells, and/or (ii) reducing hydrogen sulfide formation by said bacteria cells or other bacteria cells.   
     
     
         11 . The method of  claim 10 , further comprising:
 (d) contacting said bacteria cells or other bacteria cells comprised in a biofilm with the candidate compound identified in step (c), wherein dispersal of the biofilm indicates that the candidate compound inhibits biofilm maintenance;   (e) contacting said bacteria cells or other bacteria cells comprised in a liquid culture with the candidate compound identified in step (c), wherein an inability of the bacteria cells or other bacteria cells to form a biofilm indicates that the candidate compound inhibits biofilm formation; or   (f) contacting said bacteria cells or other bacteria cells with the candidate compound identified in step (c), wherein a reduction in hydrogen sulfide production by the bacteria cells or other bacteria cells indicates that the candidate compound inhibits hydrogen sulfide production by the bacteria cells or other bacteria cells.   
     
     
         12 . The method of  claim 10 , wherein said nucleotide sequence comprises a sequence that encodes a reporter protein, wherein increased expression of the reporter protein by the bacterial cells of step (b) indicates upregulated expression of said nucleotide sequence. 
     
     
         13 . The method of  claim 10 , wherein the DVU2956 sigma 54-dependent EBP regulatory sequence comprises a promoter sequence. 
     
     
         14 . The method of  claim 10 , wherein said bacterial cells or other bacteria cells are sulfate-reducing bacteria (sulfide-producing bacteria) cells. 
     
     
         15 . The method of  claim 10 , comprising screening a plurality of test compounds by following steps (a)-(c) to identify one or more candidate compounds for controlling bacteria cells. 
     
     
         16 . A polynucleotide comprising (i) a DVU2956 sigma 54-dependent enhancer-binding protein (EBP) regulatory sequence operably linked to (ii) a nucleotide sequence, wherein the regulatory sequence and the nucleotide sequence are heterologous to each other, optionally wherein the regulatory sequence includes a promoter sequence. 
     
     
         17 . A cell comprising the polynucleotide of  claim 16 , optionally wherein the nucleotide sequence is capable of being expressed by the cell, and preferably wherein the cell is a bacterial cell.