title: Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments.
abstract: BACKGROUND
  The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae) have been sequenced. However, no genomic data is available on the Paenibacillus species with pattern-forming and complex social motility. Here we report the de novo genome sequence of this Gram-positive, soil-dwelling, sporulating bacterium.
  
  
  RESULTS
  The complete P. vortex genome was sequenced by a hybrid approach using 454 Life Sciences and Illumina, achieving a total of 289× coverage, with 99.8% sequence identity between the two methods. The sequencing results were validated using a custom designed Agilent microarray expression chip which represented the coding and the non-coding regions. Analysis of the P. vortex genome revealed 6,437 open reading frames (ORFs) and 73 non-coding RNA genes. Comparative genomic analysis with 500 complete bacterial genomes revealed exceptionally high number of two-component system (TCS) genes, transcription factors (TFs), transport and defense related genes. Additionally, we have identified genes involved in the production of antimicrobial compounds and extracellular degrading enzymes.
  
  
  CONCLUSIONS
  These findings suggest that P. vortex has advanced faculties to perceive and react to a wide range of signaling molecules and environmental conditions, which could be associated with its ability to reconfigure and replicate complex colony architectures. Additionally, P. vortex is likely to serve as a rich source of genes important for agricultural, medical and industrial applications and it has the potential to advance the study of social microbiology within Gram-positive bacteria.
authors.affiliation: The Sackler School of Physics and Astronomy, Tel Aviv University, PO Box 39040, Tel Aviv 69978, Israel.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Sirota-Madi
authors.forename: Tsviya
authors.initials: T
authors.lastname: Olender
authors.forename: Yael
authors.initials: Y
authors.lastname: Helman
authors.forename: Colin
authors.initials: C
authors.lastname: Ingham
authors.forename: Ina
authors.initials: I
authors.lastname: Brainis
authors.forename: Dalit
authors.initials: D
authors.lastname: Roth
authors.forename: Efrat
authors.initials: E
authors.lastname: Hagi
authors.forename: Leonid
authors.initials: L
authors.lastname: Brodsky
authors.forename: Dena
authors.initials: D
authors.lastname: Leshkowitz
authors.forename: Vladimir
authors.initials: V
authors.lastname: Galatenko
authors.forename: Vladimir
authors.initials: V
authors.lastname: Nikolaev
authors.forename: Raja C
authors.initials: RC
authors.lastname: Mugasimangalam
authors.forename: Sharron
authors.initials: S
authors.lastname: Bransburg-Zabary
authors.forename: David L
authors.initials: DL
authors.lastname: Gutnick
authors.forename: Doron
authors.initials: D
authors.lastname: Lancet
authors.forename: Eshel
authors.initials: E
authors.lastname: Ben-Jacob
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D002633:Chemotaxis / Q000235:genetics; D015169:Colony Count, Microbial; D004777:Environment; D005407:Flagella / Q000235:genetics / Q000648:ultrastructure; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D009097:Multienzyme Complexes / Q000235:genetics; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D056507:Paenibacillus / Q000166:cytology / Q000235:genetics* / Q000254:growth & development* / Q000648:ultrastructure; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D009097:Multienzyme Complexes