Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri 734 013, India,
J Biosci. 2013 Nov;38(4):727-32. doi: 10.1007/s12038-013-9356-1.
Pseudogenes are defined as non-functional relatives of genes whose protein-coding abilities are lost and are no longer expressed within cells. They are an outcome of accumulation of mutations within a gene whose end product is not essential for survival. Proper investigation of the procedure of pseudogenization is relevant for estimating occurrence of duplications in genomes. Frankineae houses an interesting group of microorganisms, carving a niche in the microbial world. This study was undertaken with the objective of determining the abundance of pseudogenes, understanding strength of purifying selection, investigating evidence of pseudogene expression, and analysing their molecular nature, their origin, evolution and deterioration patterns amongst domain families. Investigation revealed the occurrence of 956 core pFAM families sharing common characteristics indicating co-evolution. WD40, Rve_3, DDE_Tnp_IS240 and phage integrase core domains are larger families, having more pseudogenes, signifying a probability of harmful foreign genes being disabled within transposable elements. High selective pressure depicted that gene families rapidly duplicating and evolving undoubtedly facilitated creation of a number of pseudogenes in Frankineae. Codon usage analysis between protein-coding genes and pseudogenes indicated a wide degree of variation with respect to different factors. Moreover, the majority of pseudogenes were under the effect of purifying selection. Frankineae pseudogenes were under stronger selective constraints, indicating that they were functional for a very long time and became pseudogenes abruptly. The origin and deterioration of pseudogenes has been attributed to selection and mutational pressure acting upon sequences for adapting to stressed soil environments.
假基因被定义为基因的非功能相关物，其编码蛋白质的能力丧失，并且在细胞内不再表达。它们是基因内突变积累的结果，其最终产物对于生存并非必需。正确研究假基因化的过程对于估计基因组中重复的发生是相关的。弗兰克氏菌门拥有一组有趣的微生物，在微生物世界中占据了一席之地。本研究旨在确定假基因的丰度，了解纯化选择的强度，研究假基因表达的证据，并分析它们的分子性质、起源、进化和在域家族中的退化模式。研究发现，存在 956 个核心 pFAM 家族，它们具有共同的特征，表明存在共同进化。WD40、Rve_3、DDE_Tnp_IS240 和噬菌体整合酶核心结构域是较大的家族，拥有更多的假基因，这表明转座元件内的有害外源基因有可能被失活。高选择压力表明，基因家族快速复制和进化无疑促进了弗兰克氏菌中大量假基因的产生。蛋白质编码基因和假基因之间的密码子使用分析表明，不同因素之间存在广泛的差异。此外，大多数假基因受到纯化选择的影响。弗兰克氏菌假基因受到更强的选择约束，表明它们在很长一段时间内是有功能的，并且突然成为了假基因。假基因的起源和退化归因于适应受胁迫土壤环境的序列受到选择和突变压力的影响。
