Österman Janina, Mousavi Seyed Abdollah, Koskinen Patrik, Paulin Lars, Lindström Kristina
Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00790, Helsinki, Finland.
Department of Environmental Sciences, University of Helsinki, Viikinkaari 2a, 00790, Helsinki, Finland.
BMC Genomics. 2015 May 2;16(1):348. doi: 10.1186/s12864-015-1576-3.
The symbiotic phenotype of Neorhizobium galegae, with strains specifically fixing nitrogen with either Galega orientalis or G. officinalis, has made it a target in research on determinants of host specificity in nitrogen fixation. The genomic differences between representative strains of the two symbiovars are, however, relatively small. This introduced a need for a dataset representing a larger bacterial population in order to make better conclusions on characteristics typical for a subset of the species. In this study, we produced draft genomes of eight strains of N. galegae having different symbiotic phenotypes, both with regard to host specificity and nitrogen fixation efficiency. These genomes were analysed together with the previously published complete genomes of N. galegae strains HAMBI 540T and HAMBI 1141.
The results showed that the presence of an additional rpoN sigma factor gene in the symbiosis gene region is a characteristic specific to symbiovar orientalis, required for nitrogen fixation. Also the nifQ gene was shown to be crucial for functional symbiosis in both symbiovars. Genome-wide analyses identified additional genes characteristic of strains of the same symbiovar and of strains having similar plant growth promoting properties on Galega orientalis. Many of these genes are involved in transcriptional regulation or in metabolic functions.
The results of this study confirm that the only symbiosis-related gene that is present in one symbiovar of N. galegae but not in the other is an rpoN gene. The specific function of this gene remains to be determined, however. New genes that were identified as specific for strains of one symbiovar may be involved in determining host specificity, while others are defined as potential determinant genes for differences in efficiency of nitrogen fixation.
东方山羊豆根瘤菌的共生表型为，其菌株分别与东方山羊豆或药用山羊豆特异性固氮，这使其成为固氮宿主特异性决定因素研究的目标。然而，这两个共生变种的代表性菌株之间的基因组差异相对较小。这就需要一个代表更大细菌群体的数据集，以便更好地推断该物种一个子集的典型特征。在本研究中，我们产生了八株具有不同共生表型的东方山羊豆根瘤菌的基因组草图，这些表型在宿主特异性和固氮效率方面均有所不同。这些基因组与先前发表的东方山羊豆根瘤菌菌株HAMBI 540T和HAMBI 1141的完整基因组一起进行了分析。
结果表明，共生基因区域中额外的rpoN sigma因子基因的存在是东方共生变种特有的特征，是固氮所必需的。nifQ基因也被证明对两个共生变种的功能共生至关重要。全基因组分析确定了同一共生变种菌株以及对东方山羊豆具有相似促进植物生长特性的菌株所特有的其他基因。其中许多基因参与转录调控或代谢功能。
本研究结果证实，东方山羊豆根瘤菌的一个共生变种中存在而另一个不存在的唯一与共生相关的基因是rpoN基因。然而，该基因的具体功能仍有待确定。被确定为一个共生变种菌株特有的新基因可能参与决定宿主特异性，而其他基因则被定义为固氮效率差异的潜在决定基因。
