Liu Shi V, Saunders Nigel J, Jeffries Alex, Rest Richard F
Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19129, USA.
J Bacteriol. 2002 Nov;184(22):6163-73. doi: 10.1128/JB.184.22.6163-6173.2002.
Whole genome sequences of Neisseria meningitidis strains Z2491 and MC58 and Neisseria gonorrhoeae FA1090 were analyzed for Correia repeats (CR) and CR-enclosed elements (CREE). A total of 533, 516, and 256 copies of CR and 270, 261, and 102 copies of CREE were found in these three genomes, respectively. The lengths of CREE range from 28 to 348 bp, and the lengths of multicopy CREE appear mainly in the ranges of 154 to 156 bp and 105 to 107 bp. The distribution of CREE lengths is similar between the two N. meningitidis genomes, with a greater number of 154- to 156-bp CREE (163 and 152 copies in N. meningitidis strain Z2491 and N. meningitidis strain MC58, respectively) than 105- to 107-bp CREE (72 and 77 copies). In the N. gonorrhoeae strain FA1090 genome there are relatively more 105- to 107-bp CREE (51 copies) than 154- to 156-bp CREE (36 copies). The genomic distribution of 107-bp CREE also shows similarity between the two N. meningitidis strains (15 copies share the same loci) and differences between N. meningitidis strains and N. gonorrhoeae FA1090 (only one copy is located in the same locus). Detailed sequence analysis showed that both the terminal inverted repeats and the core regions of CREE are composed of distinct basic sequence blocks. Direct TA dinucleotide repeats exist at the termini of all CREE. A survey of DNA sequence upstream of the sialyltransferase gene, lst, in several Neisseria isolates showed that 5 N. meningitidis strains contain a 107-bp CREE in this region but 25 N. gonorrhoeae strains show an exact absence of a 105-bp sequence block (i.e., the 107-bp CREE without a 5' TA dinucleotide) in the same region. Whole-genome sequence analysis confirmed that this 105-bp indel exists in many homologous 107-bp CREE loci. Thus, we postulate that all CREE are made of target TA with indels of various lengths. Analysis of 107-bp CREE revealed that they exist predominantly in intergenic regions and are often near virulence, metabolic, and transporter genes. The abundance of CREE in Neisseria genomes suggests that they may have played a role in genome organization, function, and evolution. Their differential distribution in different pathogenic Neisseria strains may contribute to the distinct behaviors of each Neisseria species.
对脑膜炎奈瑟菌菌株Z2491和MC58以及淋病奈瑟菌FA1090的全基因组序列进行了科雷亚重复序列（CR）和CR封闭元件（CREE）分析。在这三个基因组中分别发现了533、516和256个CR拷贝以及270、261和102个CREE拷贝。CREE的长度范围为28至348 bp，多拷贝CREE的长度主要出现在154至156 bp和105至107 bp范围内。两种脑膜炎奈瑟菌基因组中CREE长度的分布相似，154至156 bp的CREE数量更多（脑膜炎奈瑟菌菌株Z2491和脑膜炎奈瑟菌菌株MC58中分别为163和152个拷贝），而105至107 bp的CREE数量较少（分别为72和77个拷贝）。在淋病奈瑟菌FA1090基因组中，105至107 bp的CREE（51个拷贝）相对多于154至156 bp的CREE（36个拷贝）。107 bp CREE的基因组分布在两种脑膜炎奈瑟菌菌株之间也显示出相似性（15个拷贝位于相同位点），而在脑膜炎奈瑟菌菌株和淋病奈瑟菌FA1090之间存在差异（只有一个拷贝位于相同位点）。详细的序列分析表明，CREE的末端反向重复序列和核心区域均由不同的基本序列块组成。所有CREE的末端均存在直接TA二核苷酸重复序列。对几种奈瑟菌分离株中唾液酸转移酶基因lst上游的DNA序列进行的调查显示，5株脑膜炎奈瑟菌在该区域含有一个107 bp的CREE，但25株淋病奈瑟菌在同一区域完全没有105 bp的序列块（即没有5' TA二核苷酸的107 bp CREE）。全基因组序列分析证实，这种105 bp的插入缺失存在于许多同源的107 bp CREE位点。因此，我们推测所有CREE均由带有不同长度插入缺失的靶标TA组成。对107 bp CREE的分析表明，它们主要存在于基因间区域，并且常常靠近毒力、代谢和转运基因。奈瑟菌基因组中CREE的丰富性表明它们可能在基因组组织、功能和进化中发挥了作用。它们在不同致病性奈瑟菌菌株中的差异分布可能导致了每种奈瑟菌物种的独特行为。
