Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria.
Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria.
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DOI：
10.1186/gb-2003-4-2-r14
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发表时间：
2003
期刊：
影响因子：
12.3
通讯作者：
Jensen RA
中科院分区：
文献类型：
--
作者：
Xie G;Bonner CA;Brettin T;Gottardo R;Keyhani NO;Jensen RA
评估了存在于明显的操纵子样组织中的色氨酸途径基因。顶端木霉的7个基因簇显示出明显的低GC含量。这强烈地牵涉到横向基因转移。相反，参数研究和蛋白质树系统发育并不支持鱼腥藻/发菜通过侧向基因转移产生基因块。存在于一个明显的操纵子样组织内的色氨酸途径基因被评估为多基因基因组区域的例子，这些多基因基因组区域包含系统发育上不一致的基因，并与操纵子外一致的基因共存。短枝木霉的七个基因簇包括编码邻氨基苯甲酸合成酶、芳基辅酶A合成酶和Trpr的两个亚单位的基因。第二个基因片段存在于鱼腥藻/发菜谱系中，但在其他蓝藻中不存在，它包含一个近乎完整的色氨酸操纵子，嵌套在一个明显的超操纵子中，其中包含其他芳香途径基因。Fittidiosa中的基因块显示出明显的低GC含量。这一点，以及密码子使用和3：1二核苷酸分析的偏差，强烈地暗示了侧向基因转移(LGT)。相反，参数研究和蛋白质树系统发育不支持LGT产生鱼腥藻/诺斯托克基因块。从明显的微小改善来看，X.fattidiosa的低GC基因阻断可能是由LGT相对较近的时间造成的。令人惊讶的是，无法确定捐赠者的血统，这仍然为LGT以外的其他解释留下了空间，尽管可能性较小。另一方面，LGT似乎没有出现大的鱼腥藻/发菜基因块。我们认为当代发散的Anabaena/Nostoc阵列代表了一种古老的Paralog发散的祖先状态，通过代表其他(单细胞)蓝藻的后代谱系中的基因丢失进行了广泛的流线型。
Tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated. A seven-gene cluster in Xylella fastidiosa exhibits a sharply delineated low-GC content. This strongly implicates lateral gene transfer. In contrast, parametric studies and protein tree phylogenies did not support the origination of a gene block in the Anabaena/Nostoc lineage by lateral gene transfer. Tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated as examples of multi-genic genomic regions that contain phylogenetically incongruous genes and coexist with genes outside the operon that are congruous. A seven-gene cluster in Xylella fastidiosa includes genes encoding the two subunits of anthranilate synthase, an aryl-CoA synthetase, and trpR. A second gene block, present in the Anabaena/Nostoc lineage, but not in other cyanobacteria, contains a near-complete tryptophan operon nested within an apparent supraoperon containing other aromatic-pathway genes. The gene block in X. fastidiosa exhibits a sharply delineated low-GC content. This, as well as bias of codon usage and 3:1 dinucleotide analysis, strongly implicates lateral gene transfer (LGT). In contrast, parametric studies and protein tree phylogenies did not support the origination of the Anabaena/Nostoc gene block by LGT. Judging from the apparent minimal amelioration, the low-GC gene block in X. fastidiosa probably originated by LGT at a relatively recent time. The surprising inability to pinpoint a donor lineage still leaves room for alternative, albeit less likely, explanations other than LGT. On the other hand, the large Anabaena/Nostoc gene block does not seem to have arisen by LGT. We suggest that the contemporary Anabaena/Nostoc array of divergent paralogs represents an ancient ancestral state of paralog divergence, with extensive streamlining by gene loss occurring in the lineage of descent representing other (unicellular) cyanobacteria.
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影响因子：
10.7
作者：
Koski, LB;Morton, RA;Golding, GB
通讯作者：
Golding, GB
影响因子：
3.2
作者：
ESSAR, DW;EBERLY, L;CRAWFORD, IP
通讯作者：
CRAWFORD, IP
影响因子：
3.2
作者：
Gosset, G;Bonner, CA;Jensen, RA
通讯作者：
Jensen, RA
影响因子：
14.9
作者：
Maidak, BL;Cole, JR;Tiedje, JM
通讯作者：
Tiedje, JM
DOI：
10.1073/pnas.95.16.9413
发表时间：
1998-08-04
影响因子：
11.1
作者：
Lawrence, JG;Ochman, H
通讯作者：
Ochman, H