Open Access Highly Accessed Research article

Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments

Alexandra Sirota-Madi23, Tsviya Olender3, Yael Helman24, Colin Ingham5, Ina Brainis1, Dalit Roth12, Efrat Hagi4, Leonid Brodsky16, Dena Leshkowitz7, Vladimir Galatenko8, Vladimir Nikolaev9, Raja C Mugasimangalam10, Sharron Bransburg-Zabary12, David L Gutnick11, Doron Lancet3 and Eshel Ben-Jacob112*

Author Affiliations

1 The Sackler School of Physics and Astronomy, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel

2 The Sackler School of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel

3 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel

4 Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel

5 Laboratory of Microbiology, Wageningen University, Wageningen 6703 HB, Netherlands

6 Laboratory of System Biology and Analysis of High-throughput data, Institute of Evolution, University of Haifa, Haifa 31905, Israel

7 Department of Biological Services, Weizmann Institute of Science, Rehovot 76100, Israel

8 Department of Mathematical Analysis, Faculty of Mechanics and Mathematics, Moscow State University, Moscow 119991, Russia

9 A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia

10 Genotypic Technology (P) Ltd, Bangalore 560094, India

11 Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel

12 The Center for Theoretical and Biological Physics, University of California San Diego, La Jolla, California 92093, USA

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BMC Genomics 2010, 11:710  doi:10.1186/1471-2164-11-710

Published: 17 December 2010

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.