LDSS-P: an advanced algorithm to extract functional short motifs associated with coordinated gene expression

Nucleic Acids Res. 2016 Jun 20;44(11):5045-53. doi: 10.1093/nar/gkw435. Epub 2016 May 17.


Identifying functional elements in promoter sequences is a major goal in computational and experimental genome biology. Here, we describe an algorithm, Local Distribution of Short Sequences for Prokaryotes (LDSS-P), to identify conserved short motifs located at specific positions in the promoters of co-expressed prokaryotic genes. As a test case, we applied this algorithm to a symbiotic nitrogen-fixing bacterium, Sinorhizobium meliloti The LDSS-P profiles that overlap with the 5' section of the extracytoplasmic function RNA polymerase sigma factor RpoE2 consensus sequences displayed a sharp peak between -34 and -32 from TSS positions. The corresponding genes overlap significantly with RpoE2 targets identified from previous experiments. We further identified several groups of genes that are co-regulated with characterized marker genes. Our data indicate that in S. meliloti, and possibly in other Rhizobiaceae species, the master cell cycle regulator CtrA may recognize an expanded motif (AACCAT), which is positionally shifted from the previously reported CtrA consensus sequence in Caulobacter crescentus Bacterial one-hybrid experiments showed that base substitution in the expanded motif either increase or decrease the binding by CtrA. These results show the effectiveness of LDSS-P as a method to delineate functional promoter elements.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions
  • Algorithms*
  • Base Sequence
  • Computational Biology / methods*
  • Consensus Sequence*
  • Conserved Sequence
  • Gene Expression Regulation, Bacterial
  • Molecular Sequence Annotation
  • Nucleotide Motifs*
  • Position-Specific Scoring Matrices
  • Prokaryotic Cells*
  • Promoter Regions, Genetic
  • Sinorhizobium meliloti / genetics
  • Sinorhizobium meliloti / metabolism
  • Software*
  • Web Browser


  • 5' Untranslated Regions