Saha Deeya, Podder Soumita, Panda Arup, Ghosh Tapash Chandra
Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India.
Gene. 2016 May 15;582(2):143-7. doi: 10.1016/j.gene.2016.02.002. Epub 2016 Feb 4.
Elucidating the genomic features influencing prokaryotic growth rates has always been a study of interest. Previously, it was observed that overlapping genes (OGs) play a crucial role in the prokaryotic genome size reduction. This study is focused to explore whether OGs act as a potential correlate of prokaryotic growth rates. For this purpose, we compiled a dataset of 25 archaeal and 117 eubacterial genomes and analyzed the inter-correlation between the proportion of overlapping regions in these genomes with their growth rates. Here, we observed that the proportion of overlapping region holds a significant negative correlation with generation time in archaeal domain, whereas no correlation was observed in the eubacterial domain. However, after masking the effect of tRNA, rRNA multiplicity and environmental diversity, OGs show an independent effect over growth rates in the eubacterial domain as well as in the archaeal domain. Moreover, the influence of OGs on prokaryotic growth rates provides different delineations in archaeal and eubacterial domains. In archaea, both long overlap frequency (LOF) and short overlap frequency (SOF) influence the growth rates by increasing the degree of operonization. On the contrary, in the case of bacteria, neither SOF nor LOF plays any significant role in achieving faster growth rates.
阐明影响原核生物生长速率的基因组特征一直是一项备受关注的研究。此前，人们观察到重叠基因（OGs）在原核生物基因组大小缩减中起着关键作用。本研究旨在探讨OGs是否作为原核生物生长速率的潜在相关因素。为此，我们编制了一个包含25个古菌基因组和117个真细菌基因组的数据集，并分析了这些基因组中重叠区域比例与其生长速率之间的相互关系。在此，我们观察到重叠区域比例在古菌域与世代时间呈显著负相关，而在真细菌域未观察到相关性。然而，在消除tRNA、rRNA多样性和环境多样性的影响后，OGs在真细菌域以及古菌域均对生长速率显示出独立影响。此外，OGs对原核生物生长速率的影响在古菌域和真细菌域呈现出不同的情况。在古菌中，长重叠频率（LOF）和短重叠频率（SOF）均通过增加操纵子化程度来影响生长速率。相反，在细菌中，SOF和LOF在实现更快生长速率方面均未发挥任何显著作用。
