Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility.
Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven "central aromatic" and twenty "peripheral aromatic" pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.
Chain
Patrick S G
PS
Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA.
Denef
Vincent J
VJ
Konstantinidis
Konstantinos T
KT
Vergez
Lisa M
LM
Agulló
Loreine
L
Reyes
Valeria Latorre
VL
Hauser
Loren
L
Córdova
Macarena
M
Gómez
Luis
L
González
Myriam
M
Land
Miriam
M
Lao
Victoria
V
Larimer
Frank
F
LiPuma
John J
JJ
Mahenthiralingam
Eshwar
E
Malfatti
Stephanie A
SA
Marx
Christopher J
CJ
Parnell
J Jacob
JJ
Ramette
Alban
A
Richardson
Paul
P
Seeger
Michael
M
Smith
Daryl
D
Spilker
Theodore
T
Sul
Woo Jun
WJ
Tsoi
Tamara V
TV
Ulrich
Luke E
LE
Zhulin
Igor B
IB
Tiedje
James M
JM
D019117:Burkholderia / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D002876:Chromosomes, Bacterial; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D015394:Molecular Structure; D020411:Oligonucleotide Array Sequence Analysis; D012093:Replicon