Tokajian Sima, Issa Nahla, Salloum Tamara, Ibrahim Joe, Farah Maya
Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Byblos, Lebanon.
Front Microbiol. 2016 Feb 11;7:149. doi: 10.3389/fmicb.2016.00149. eCollection 2016.
Sphingomonads comprise a physiologically versatile group many of which appear to be adapted to oligotrophic environments, but several also had features in their genomes indicative of host associations. In this study, the extent variability of the 16S-23S rDNA intergenic spacer (ITS) sequences of 14 ATCC reference sphingomonad strains and 23 isolates recovered from drinking water was investigated through PCR amplification and sequencing. Sequencing analysis of the 16S-23S rRNA gene ITS region revealed that the ITS sizes for all studied isolates varied between 415 and 849 bp, while their G+C content was 42.2-57.9 mol%. Five distinct ITS types were identified: ITS(none) (without tRNA genes), ITS(Ala(TGC)), ITS(Ala(TGC)+Ile(GAT)), ITS(Ile(GAT)+Ala(TGC)), and ITS (Ile(GAT)+Pseudo). All of the identified tRNA(Ala(TGC)) molecules consisted of 73 bases, and all of the tRNA(Ile(GAT)) molecules consisted of 74 bases. We also detected striking variability in the size of the ITS region among the various examined isolates. Highest variability was detected within the ITS-2. The importance of this study is that this is the first comparison of the 16S-23S rDNA ITS sequence similarities and tRNA genes from sphingomonads. Collectively the data obtained in this study revealed the heterogeneity and extent of variability within the ITS region compared to the 16S rRNA gene within closely related isolates. Sequence and length polymorphisms within the ITS region along with the ITS types (tRNA-containing or lacking and the type of tRNA) and ITS-2 size and sequence similarities allowed us to overcome the limitation we previously encountered in resolving closely related isolates based on the 16S rRNA gene sequence.
鞘氨醇单胞菌属包含一组生理功能多样的菌群，其中许多似乎适应贫营养环境，但也有一些在其基因组中具有表明与宿主相关的特征。在本研究中，通过聚合酶链反应（PCR）扩增和测序，对14株美国典型培养物保藏中心（ATCC）参考鞘氨醇单胞菌菌株和从饮用水中分离出的23株菌株的16S - 23S核糖体DNA（rDNA）基因间隔区（ITS）序列的变异程度进行了研究。对16S - 23S核糖体RNA（rRNA）基因ITS区域的测序分析表明，所有研究菌株的ITS大小在415至849碱基对（bp）之间，而其鸟嘌呤和胞嘧啶（G + C）含量为42.2 - 57.9摩尔%。鉴定出五种不同的ITS类型：ITS（无）（不含转运RNA（tRNA）基因）、ITS（丙氨酸（TGC））、ITS（丙氨酸（TGC）+异亮氨酸（GAT））、ITS（异亮氨酸（GAT）+丙氨酸（TGC））和ITS（异亮氨酸（GAT）+假基因）。所有鉴定出的tRNA（丙氨酸（TGC））分子由73个碱基组成，所有tRNA（异亮氨酸（GAT））分子由74个碱基组成。我们还在各种检测菌株中检测到ITS区域大小的显著变异。在ITS - 2内检测到最高的变异性。本研究的重要性在于，这是首次对鞘氨醇单胞菌的16S - 23S rDNA ITS序列相似性和tRNA基因进行比较。总体而言，本研究获得的数据揭示了与密切相关菌株中的16S rRNA基因相比，ITS区域内的异质性和变异程度。ITS区域内的序列和长度多态性以及ITS类型（含或不含tRNA以及tRNA的类型）和ITS - 2大小及序列相似性使我们能够克服之前在基于16S rRNA基因序列解析密切相关菌株时遇到的局限性。
