Ast Jennifer C, Urbanczyk Henryk, Dunlap Paul V
Department of Ecological and Evolutionary Biology, University of Michigan, 830 North University Ave., Ann Arbor, MI 48109-1048, USA.
J Bacteriol. 2007 Sep;189(17):6148-58. doi: 10.1128/JB.00672-07. Epub 2007 Jun 22.
Sequence analysis of the bacterial luminescence (lux) genes has proven effective in helping resolve evolutionary relationships among luminous bacteria. Phylogenetic analysis using lux genes, however, is based on the assumptions that the lux genes are present as single copies on the bacterial chromosome and are vertically inherited. We report here that certain strains of Photobacterium leiognathi carry multiple phylogenetically distinct copies of the entire operon that codes for luminescence and riboflavin synthesis genes, luxCDABEG-ribEBHA. Merodiploid lux-rib strains of P. leiognathi were detected during sequence analysis of luxA. To define the gene content, organization, and sequence of each lux-rib operon, we constructed a fosmid library of genomic DNA from a representative merodiploid strain, lnuch.13.1. Sequence analysis of fosmid clones and genomic analysis of lnuch.13.1 defined two complete, physically separate, and apparently functional operons, designated lux-rib1 and lux-rib2. P. leiognathi strains lelon.2.1 and lnuch.21.1 were also found to carry lux-rib1 and lux-rib2, whereas ATCC 25521T apparently carries only lux-rib1. In lnuch.13.1, lelon.2.1, lnuch.21.1, and ATCC 25521T, lux-rib1 is flanked upstream by lumQ and putA and downstream by a gene for a hypothetical multidrug efflux pump. In contrast, transposase genes flank lux-rib2 of lnuch.13.1, and the chromosomal location of lux-rib2 apparently differs in lnuch.13.1, lelon.2.1, and lnuch.21.1. Phylogenetic analysis demonstrated that lux-rib1 and lux-rib2 are more closely related to each other than either one is to the lux and rib genes of other bacterial species, which rules out interspecies lateral gene transfer as the origin of lux-rib2 in P. leiognathi; lux-rib2 apparently arose within a previously unsampled or extinct P. leiognathi lineage. Analysis of 170 additional strains of P. leiognathi, for a total of 174 strains examined from coastal waters of Japan, Taiwan, the Philippine Islands, and Thailand, identified 106 strains that carry only a single lux-rib operon and 68 that carry multiple lux-rib operons. Strains bearing a single lux-rib operon were obtained throughout the geographic sampling range, whereas lux-rib merodiploid strains were found only in coastal waters of central Honshu. This is the first report of merodiploidy of lux or rib genes in a luminous bacterium and the first indication that a natural merodiploid state in bacteria can correlate with geography.
细菌发光（lux）基因的序列分析已被证明有助于解析发光细菌之间的进化关系。然而，使用lux基因进行的系统发育分析基于这样的假设：lux基因以单拷贝形式存在于细菌染色体上并垂直遗传。我们在此报告，某些利氏发光杆菌菌株携带编码发光和核黄素合成基因（luxCDABEG - ribEBHA）的整个操纵子的多个系统发育上不同的拷贝。在对luxA进行序列分析期间检测到了利氏发光杆菌的部分二倍体lux - rib菌株。为了确定每个lux - rib操纵子的基因组成、组织和序列，我们构建了来自代表性部分二倍体菌株lnuch.13.1的基因组DNA的fosmid文库。fosmid克隆的序列分析和lnuch.13.1的基因组分析确定了两个完整的、物理上分离的且显然有功能的操纵子，命名为lux - rib1和lux - rib2。还发现利氏发光杆菌菌株lelon.2.1和lnuch.21.1也携带lux - rib1和lux - rib2，而ATCC 25521T显然只携带lux - rib1。在lnuch.13.1、lelon.2.1、lnuch.21.1和ATCC 25521T中，lux - rib1的上游侧翼是lumQ和putA，下游是一个假定的多药外排泵基因。相比之下，lnuch.13.1的lux - rib2侧翼是转座酶基因，并且lux - rib2在lnuch.13.1、lelon.2.1和lnuch.21.1中的染色体位置显然不同。系统发育分析表明，lux - rib1和lux - rib2彼此之间的关系比它们与其他细菌物种的lux和rib基因的关系更密切，这排除了种间横向基因转移是利氏发光杆菌中lux - rib2的起源；lux - rib2显然是在一个先前未采样或已灭绝的利氏发光杆菌谱系中产生的。对另外170株利氏发光杆菌进行分析，总共检测了来自日本、台湾、菲律宾群岛和泰国沿海水域的174株菌株，发现106株只携带一个lux - rib操纵子，68株携带多个lux - rib操纵子。携带单个lux - rib操纵子的菌株在整个地理采样范围内都有获得，而lux - rib部分二倍体菌株仅在本州中部的沿海水域中发现。这是关于发光细菌中lux或rib基因部分二倍体现象的首次报告，也是细菌中自然部分二倍体状态与地理分布相关的首个迹象。
