Endo Akihito, Tanizawa Yasuhiro, Tanaka Naoto, Maeno Shintaro, Kumar Himanshu, Shiwa Yuh, Okada Sanae, Yoshikawa Hirofumi, Dicks Leon, Nakagawa Junichi, Arita Masanori
Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido, 099-2493, Japan.
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
BMC Genomics. 2015 Dec 29;16:1117. doi: 10.1186/s12864-015-2339-x.
Fructobacillus spp. in fructose-rich niches belong to the family Leuconostocaceae. They were originally classified as Leuconostoc spp., but were later grouped into a novel genus, Fructobacillus, based on their phylogenetic position, morphology and specific biochemical characteristics. The unique characters, so called fructophilic characteristics, had not been reported in the group of lactic acid bacteria, suggesting unique evolution at the genome level. Here we studied four draft genome sequences of Fructobacillus spp. and compared their metabolic properties against those of Leuconostoc spp.
Fructobacillus species possess significantly less protein coding sequences in their small genomes. The number of genes was significantly smaller in carbohydrate transport and metabolism. Several other metabolic pathways, including TCA cycle, ubiquinone and other terpenoid-quinone biosynthesis and phosphotransferase systems, were characterized as discriminative pathways between the two genera. The adhE gene for bifunctional acetaldehyde/alcohol dehydrogenase, and genes for subunits of the pyruvate dehydrogenase complex were absent in Fructobacillus spp. The two genera also show different levels of GC contents, which are mainly due to the different GC contents at the third codon position.
The present genome characteristics in Fructobacillus spp. suggest reductive evolution that took place to adapt to specific niches.
存在于富含果糖生态位中的果糖杆菌属属于明串珠菌科。它们最初被归类为明串珠菌属，但后来基于系统发育位置、形态和特定生化特征被归入一个新属——果糖杆菌属。这种独特的特征，即所谓的嗜果糖特性，在乳酸菌群体中尚未见报道，这表明在基因组水平上存在独特的进化。在此，我们研究了果糖杆菌属的四个基因组草图序列，并将它们的代谢特性与明串珠菌属的代谢特性进行了比较。
果糖杆菌属物种在其较小的基因组中拥有显著更少的蛋白质编码序列。碳水化合物转运和代谢方面的基因数量显著更少。其他几种代谢途径，包括三羧酸循环、泛醌和其他萜类醌生物合成以及磷酸转移酶系统，被确定为这两个属之间的判别途径。果糖杆菌属中不存在用于双功能乙醛/醇脱氢酶的adhE基因以及丙酮酸脱氢酶复合体亚基的基因。这两个属还表现出不同水平的GC含量，这主要是由于第三个密码子位置的GC含量不同所致。
果糖杆菌属目前的基因组特征表明其发生了适应性进化以适应特定生态位。
