Word frequency distribution under restriction avoidance

限制回避下的词频分布

• 批准号: 14540581
• 负责人: SASAKI Akira
• 金额: $ 2.24万
• 依托单位: Kyushu University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2002
• 资助国家: 日本
• 起止时间: 2002 至 2003
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-14540581/
• 关键词: restriction avoidance; phage escape; word frequency; mutation load; substitution load; fitness landscape; recognition sequence; palindrome; 制限修飾酵素; ファージエスケープ; DNA結合タンパク質; ワード分布; 擬種分布; エラーカタストロフ; 有限オートマトン; 制限・修飾酵素; バクテリア; 共進化; 塩基配列

Restriction enzymes of bacteria cut the unmodified recognition sites of DNA, thereby protect bacteria from their parasites. This potentially imposes strong selection on phage genome sequences.. To answer the evolution of phage genome under the selection by bacteria restriction enzymes, a simple model for the evolution of binary sequences is proposed. The model shows that not only the restricted sequence itself but the relative abundance of associated subsequences (words) in the genome will be largely deviated from the random expectations. The word frequency distribution sensitively depends on the type of restricted sequence. If the restricted sequence is of m type, where x is either 0 or 1, the frequency of a 3-letter word is largely explained by its Hamming distance from the restricted sequence -the farther is the Hamming distance from restriction sequence, the more is the abundance of that subsequence. However, quite unexpected word frequency distribution arises if the restricted sequence is of xxy or xyx type. The abundance of words is largely influenced by the vulnerability to restriction of partially overlapped adjacent words. For example, when 001 is the restriction sequence, the word 100, which is two steps distant from the restriction sequence, becomes quite rare in the genome. Such distribution of words under restriction is well explained by counting the relative abundance of words in the feasible sequences, which are the sequences without any restriction site. Simple formula for the word distribution in the feasible sequences are obtained.

细菌的限制性内切酶切割DNA的未修饰识别位点，从而保护细菌免受寄生虫的侵害。这潜在地对噬菌体基因组序列施加强选择。为了回答细菌限制性内切酶选择下噬菌体基因组的进化问题，提出了一个简单的二元序列进化模型。该模型表明，不仅限制性序列本身，而且基因组中相关序列（单词）的相对丰度将在很大程度上偏离随机预期。词频分布敏感地依赖于限制序列的类型。如果限制性序列是m类型的，其中x是0或1，则3个字母的单词的频率在很大程度上由其与限制性序列的汉明距离来解释-距离限制性序列的汉明距离越远，该子序列的丰度越大。然而，如果限制序列是xxy或xyx类型的，则会出现非常意想不到的词频分布。词的丰富性在很大程度上受到部分重叠的相邻词对限制的脆弱性的影响。例如，当001是限制性序列时，距离限制性序列两步的单词100在基因组中变得非常罕见。这种限制下的词的分布可以通过计算可行序列中词的相对丰度来很好地解释，可行序列是没有任何限制位点的序列。得到了可行序列中字分布的简单公式。

项目成果

Kawaguchi I, Sasaki A, Mogi TM: "Combining zooprophylaxis and insecticide spraying : a malaria-control strategy limiting the development of insecticide resistance in vector mosquitoes"Proc.Roy.Soc.Lond.B. 271. 301-309 (2003)

Kawaguchi I、Sasaki A、Mogi TM：“结合动物预防和杀虫剂喷洒：一种限制媒介蚊子产生杀虫剂抗药性的疟疾控制策略”Proc.Roy.Soc.Lond.B。

Kamo M, Sasaki A: "The effect of cross-immunity and seasonal forcing in multi-strain epidemic model"Physica D. 065. 228-241 (2002)

Kamo M、Sasaki A：“多毒株流行模型中交叉免疫和季节强迫的影响”Physica D. 065. 228-241 (2002)

Nowak M A, Sasaki A, Taylor C, Fudenberg D: "Emergence of cooperation and evolutionary stability in finite populations"Nature. 428. 646-650 (2004)

Nowak M A、Sasaki A、Taylor C、Fudenberg D：“有限种群中合作的出现和进化稳定性”自然。

Krakauer D C, Sasaki A: "Noisy clues to the origin of life"Proc.Roy.Soc.Lond.B. 269. 2423-2428 (2002)

Krakauer D C、Sasaki A：“生命起源的嘈杂线索”Proc.Roy.Soc.Lond.B。

Boots M, Sasaki A: "Evolution of sexually and vector transmitted diseases"Ecology Letters. (in press).

Boots M，Sasaki A：“性传播疾病和媒介传播疾病的进化”生态学快报。