Malumbres M, Gil J A, Martín J F
Department of Ecology, Genetics and Microbiology, Faculty of Biology, University of León, Spain.
Gene. 1993 Nov 30;134(1):15-24. doi: 10.1016/0378-1119(93)90169-4.
The codon usage (CU) of 34 genes from the closely related species, Brevibacterium lactofermentum and Corynebacterium glutamicum (BLCG), was analysed and compared with that of 23 genes from other Brevibacterium and Corynebacterium species. The G+C content of the BLCG genes ranged from 50 to 62%. A wider range was found in other corynebacterial genes (25-71%). The G+C contents of non-coding regions in glutamic acid bacteria are lower than those of the coding regions and both values are lower than the G+C content of ribosomal RNA (rRNA) sequences, suggesting an unusual biased mutation pressure. The CU and synonymous codon usage (SCU) analysis showed several common characteristics among the sequenced corynebacterial genes, consistent with the close relatedness of B. lactofermentum and C. glutamicum. A subset of 25 preferred codons were deduced from the presumably highly expressed genes and they encode most of the amino acid (aa) residues of the BLCG group. An analysis of the effective number of codons (Nc) was carried out in order to check the GC3s (G+C content at the silent third position of sense codons) dependence of the CU in corynebacteria. Nc values showed differences between the BLCG group and other corynebacterial sequences. A comparison of the most used codons for each aa showed a stronger similarity to Streptomyces than to Escherichia coli. The CU/SCU tables of corynebacteria are useful for identification of protein-coding regions, including start codons when they are uncertain, and for designing oligodeoxyribonucleotide probes from an aa sequence.
分析了密切相关的乳酸发酵短杆菌和谷氨酸棒杆菌（BLCG）的34个基因的密码子使用情况（CU），并与其他短杆菌属和棒杆菌属物种的23个基因进行了比较。BLCG基因的G+C含量范围为50%至62%。在其他棒杆菌基因中发现了更广泛的范围（25%-71%）。谷氨酸细菌非编码区的G+C含量低于编码区，且两者的值均低于核糖体RNA（rRNA）序列的G+C含量，这表明存在异常的偏向性突变压力。CU和同义密码子使用情况（SCU）分析显示，在已测序的棒杆菌基因中有几个共同特征，这与乳酸发酵短杆菌和谷氨酸棒杆菌的密切相关性一致。从推测为高表达的基因中推导了25个偏好密码子的子集，它们编码了BLCG组的大部分氨基酸（aa）残基。为了检查棒杆菌中CU对GC3s（有义密码子沉默第三位的G+C含量）的依赖性，进行了有效密码子数（Nc）分析。Nc值在BLCG组和其他棒杆菌序列之间存在差异。对每个aa最常用密码子的比较表明，与链霉菌的相似性比对大肠杆菌的更强。棒杆菌的CU/SCU表可用于鉴定蛋白质编码区，包括起始密码子不确定时的起始密码子，以及从aa序列设计寡脱氧核糖核苷酸探针。
