本文对蒺藜苜蓿叶绿体基因组全序列密码子进行分析，筛选出50条CDS（coding DNA sequence）利用Codo-nW软件进行分析其密码子使用模式。结果显示，蒺藜苜蓿叶绿体基因组密码子第3位碱基GC含量为26．9％，即第3位密码子富含A和U，ENC值...本文对蒺藜苜蓿叶绿体基因组全序列密码子进行分析，筛选出50条CDS（coding DNA sequence）利用Codo-nW软件进行分析其密码子使用模式。结果显示，蒺藜苜蓿叶绿体基因组密码子第3位碱基GC含量为26．9％，即第3位密码子富含A和U，ENC值在37．11～51．91之间密码子偏好性较弱。相对同义密码子使用度分析显示RSCU值大于1的密码子有23个，其中以A和U为结尾20个。中性绘图分析显示GC12与GC3的相关系数为0．341，相关性不显著，回归系数为0．4843；单基因ENC比值多分布在-0．05～0．05，即大部分基因ENC值离ENC期望值较近；对应性分析，第一轴显示了12．50％的差异为主要影响因素，第一轴与ENC和GC。的相关系数分别为0．091和-0．092，均相关不显著。综合这几项分析发现蒺藜苜蓿叶绿体基因组密码子偏好性主要受到突变的影响，但是并不是唯一的影响因素，其他因素对密码子偏好性也可能有一定的影响。最终通过高表达优越密码子方法确定得出UUA、UUG、CCU等23个密码子为最优密码子，为之后对外源基因进行改造，提高其在叶绿体中的表达效率奠定了基础。展开更多
为了利用叶绿体基因工程技术改良普通油茶的重要经济性状,该研究以普通油茶叶绿体全基因组序列为材料,从中筛选出51条长度大于300 bp且以ATG起始的非重复CDS(Coding DNA Sequence)为对象,利用CodonW软件分析其密码子偏好性。结果表明:...为了利用叶绿体基因工程技术改良普通油茶的重要经济性状,该研究以普通油茶叶绿体全基因组序列为材料,从中筛选出51条长度大于300 bp且以ATG起始的非重复CDS(Coding DNA Sequence)为对象,利用CodonW软件分析其密码子偏好性。结果表明:密码子第三位GC含量为27.55%,ENC范围在35.23~56.67之间,平均值为46.09;RSCU值大于1.00的密码子数目为30个,其中29个第三位碱基以U或A结尾;中性绘图表明GC12与GC3的相关系数为0.143,相关性不显著,回归系数为0.0573;频数分布显示,55%基因的ENC比值集中分布在0~0.1,25%基因的ENC比值分布在0.1~0.2之间;对应分析结果表明,第一向量轴占10.12%的差异,第二向量轴占9.36%的差异,其余两轴分别占7.97%和7.46%,前4轴累计差异为34.91%。中性绘图、ENC-plot和对应性分析均表明普通油茶叶绿体基因密码子偏好受突变作用,更多受选择的影响。最终取高表达优越密码子和高频密码子共有的CUU、AUU、GUU、GUA、UAA、CAA、AAA、GAC、GAA、CCU、ACU、GCU、GCA、UGU、CGU、AGU、UUG、GGU等18个密码子作为最优密码子。该研究结果为利用叶绿体基因工程技术改良普通油茶重要经济性状奠定了基础。展开更多
In many organisms, the difference in codon usage patterns among genes reflects variation in local base compositional biases and the intensity of natural selection. In this study, a comparative analysis was performed t...In many organisms, the difference in codon usage patterns among genes reflects variation in local base compositional biases and the intensity of natural selection. In this study, a comparative analysis was performed to investigate the characteristics of codon bias and factors in shaping the codon usage patterns among mitochondrion, chloroplast and nuclear genes in common wheat （Triticum aestivum L.）. GC contents in nuclear genes were higher than that in mitochondrion and chloroplast genes. The neutrality and correspondence analyses indicated that the codon usage in nuclear genes would be a result of relative strong mutational bias, while the codon usage patterns of mitochondrion and chloroplast genes were more conserved in GC content and influenced by translation level. The Parity Rule 2 （PR2） plot analysis showed that pyrimidines were used more frequently than purines at the third codon position in the three genomes. In addition, using a new alterative strategy, 11, 12, and 24 triplets were defined as preferred codons in the mitochondrion, chloroplast and nuclear genes, respectively. These findings suggested that the mitochondrion, chloroplast and nuclear genes shared particularly different features of codon usage and evolutionary constraints.展开更多
Leaf senescence, a type of programmed cell death （PCD） characterized by chlorophyll degradation, is important to plant growth and crop productivity. It emerges that autophagy is involved in chloroplast degradation d...Leaf senescence, a type of programmed cell death （PCD） characterized by chlorophyll degradation, is important to plant growth and crop productivity. It emerges that autophagy is involved in chloroplast degradation during leaf senescence. However, the molecular mechanism（s） involved in the process is not well understood. In this study, the genetic and physiological characteristics Of the rice rlsl （rapid leaf senescence 1） mutant were identified. The rlsl mutant developed small, yellow-brown lesions resembling disease scattered over the whole surfaces of leaves that displayed earlier senescence than those of wild-type plants. The rapid loss of chlorophyll content during senescence was the main cause of accelerated leaf senescence in rlsl. Microscopic observation indicated that PCD was misregulated, probably resulting in the accelerated degradation of chloroplasts in rlsl leaves. Map-based cloning of the RLS1 gene revealed that it encodes a pre- viously uncharacterized NB （nucleotide-binding site）-containing protein with an ARM （armadillo） domain at the carboxyl terminus. Consistent with its involvement in leaf senescence, RLS1 was up-regulated during dark-induced leaf senescence and down-regulated by cytokinin. Intriguingly, constitutive expression of RLS1 also slightly accelerated leaf senescence with decreased chlorophyll content in transgenic rice plants. Our study identified a previously uncharacterized NB-ARM protein involved in PCD during plant growth and development, providing a unique tool for dissecting possible autophagy- mediated PCD during senescence in plants.展开更多
在100 mm o l/L N aC l胁迫下,研究了外源多胺-腐胺(Pu t)、尸胺(C ad)、亚精胺(Spd)和精胺(Spm)对玉米幼苗生长、光合速率和PSⅡ光化学效率(Fv/Fm)、叶绿体结合多胺和叶片丙二醛(M DA)含量以及抗氧化酶活性的影响.结果表明,叶面喷施1 m...在100 mm o l/L N aC l胁迫下,研究了外源多胺-腐胺(Pu t)、尸胺(C ad)、亚精胺(Spd)和精胺(Spm)对玉米幼苗生长、光合速率和PSⅡ光化学效率(Fv/Fm)、叶绿体结合多胺和叶片丙二醛(M DA)含量以及抗氧化酶活性的影响.结果表明,叶面喷施1 mm o l/L的Pu t、Spd和Spm可显著增加盐胁迫下玉米幼苗干物质重、叶绿体内结合态多胺的含量、叶片净光合速率和PSⅡ光化学效率(Fv/Fm),并降低了叶片中M DA含量.外源Spd和Spm明显增加盐胁迫下玉米幼苗的抗坏血酸过氧化物酶(APX)、过氧化物酶(POD)和过氧化氢酶(CAT)活性;外源Pu t可增强APX和POD活性,对CAT活性的影响不明显.这些结果表明多胺对玉米盐害的缓解作用可能是由于提高了叶绿体中结合态多胺的含量和叶片抗氧化酶的活性,从而增强了盐胁迫下的玉米光合能力.展开更多
文摘本文对蒺藜苜蓿叶绿体基因组全序列密码子进行分析，筛选出50条CDS（coding DNA sequence）利用Codo-nW软件进行分析其密码子使用模式。结果显示，蒺藜苜蓿叶绿体基因组密码子第3位碱基GC含量为26．9％，即第3位密码子富含A和U，ENC值在37．11～51．91之间密码子偏好性较弱。相对同义密码子使用度分析显示RSCU值大于1的密码子有23个，其中以A和U为结尾20个。中性绘图分析显示GC12与GC3的相关系数为0．341，相关性不显著，回归系数为0．4843；单基因ENC比值多分布在-0．05～0．05，即大部分基因ENC值离ENC期望值较近；对应性分析，第一轴显示了12．50％的差异为主要影响因素，第一轴与ENC和GC。的相关系数分别为0．091和-0．092，均相关不显著。综合这几项分析发现蒺藜苜蓿叶绿体基因组密码子偏好性主要受到突变的影响，但是并不是唯一的影响因素，其他因素对密码子偏好性也可能有一定的影响。最终通过高表达优越密码子方法确定得出UUA、UUG、CCU等23个密码子为最优密码子，为之后对外源基因进行改造，提高其在叶绿体中的表达效率奠定了基础。
文摘为了利用叶绿体基因工程技术改良普通油茶的重要经济性状,该研究以普通油茶叶绿体全基因组序列为材料,从中筛选出51条长度大于300 bp且以ATG起始的非重复CDS(Coding DNA Sequence)为对象,利用CodonW软件分析其密码子偏好性。结果表明:密码子第三位GC含量为27.55%,ENC范围在35.23~56.67之间,平均值为46.09;RSCU值大于1.00的密码子数目为30个,其中29个第三位碱基以U或A结尾;中性绘图表明GC12与GC3的相关系数为0.143,相关性不显著,回归系数为0.0573;频数分布显示,55%基因的ENC比值集中分布在0~0.1,25%基因的ENC比值分布在0.1~0.2之间;对应分析结果表明,第一向量轴占10.12%的差异,第二向量轴占9.36%的差异,其余两轴分别占7.97%和7.46%,前4轴累计差异为34.91%。中性绘图、ENC-plot和对应性分析均表明普通油茶叶绿体基因密码子偏好受突变作用,更多受选择的影响。最终取高表达优越密码子和高频密码子共有的CUU、AUU、GUU、GUA、UAA、CAA、AAA、GAC、GAA、CCU、ACU、GCU、GCA、UGU、CGU、AGU、UUG、GGU等18个密码子作为最优密码子。该研究结果为利用叶绿体基因工程技术改良普通油茶重要经济性状奠定了基础。
基金Supported by the Sate Key Basic Research and Development Plan of China （2003CB715904） and the National Science Foundation for 0verseas Distinguished Young Scholar （30428003）
文摘In many organisms, the difference in codon usage patterns among genes reflects variation in local base compositional biases and the intensity of natural selection. In this study, a comparative analysis was performed to investigate the characteristics of codon bias and factors in shaping the codon usage patterns among mitochondrion, chloroplast and nuclear genes in common wheat （Triticum aestivum L.）. GC contents in nuclear genes were higher than that in mitochondrion and chloroplast genes. The neutrality and correspondence analyses indicated that the codon usage in nuclear genes would be a result of relative strong mutational bias, while the codon usage patterns of mitochondrion and chloroplast genes were more conserved in GC content and influenced by translation level. The Parity Rule 2 （PR2） plot analysis showed that pyrimidines were used more frequently than purines at the third codon position in the three genomes. In addition, using a new alterative strategy, 11, 12, and 24 triplets were defined as preferred codons in the mitochondrion, chloroplast and nuclear genes, respectively. These findings suggested that the mitochondrion, chloroplast and nuclear genes shared particularly different features of codon usage and evolutionary constraints.
基金This work was supported by grants from the National Natural Science Foundation of China，the National Key Basic Research and Development Program
文摘Leaf senescence, a type of programmed cell death （PCD） characterized by chlorophyll degradation, is important to plant growth and crop productivity. It emerges that autophagy is involved in chloroplast degradation during leaf senescence. However, the molecular mechanism（s） involved in the process is not well understood. In this study, the genetic and physiological characteristics Of the rice rlsl （rapid leaf senescence 1） mutant were identified. The rlsl mutant developed small, yellow-brown lesions resembling disease scattered over the whole surfaces of leaves that displayed earlier senescence than those of wild-type plants. The rapid loss of chlorophyll content during senescence was the main cause of accelerated leaf senescence in rlsl. Microscopic observation indicated that PCD was misregulated, probably resulting in the accelerated degradation of chloroplasts in rlsl leaves. Map-based cloning of the RLS1 gene revealed that it encodes a pre- viously uncharacterized NB （nucleotide-binding site）-containing protein with an ARM （armadillo） domain at the carboxyl terminus. Consistent with its involvement in leaf senescence, RLS1 was up-regulated during dark-induced leaf senescence and down-regulated by cytokinin. Intriguingly, constitutive expression of RLS1 also slightly accelerated leaf senescence with decreased chlorophyll content in transgenic rice plants. Our study identified a previously uncharacterized NB-ARM protein involved in PCD during plant growth and development, providing a unique tool for dissecting possible autophagy- mediated PCD during senescence in plants.
文摘在100 mm o l/L N aC l胁迫下,研究了外源多胺-腐胺(Pu t)、尸胺(C ad)、亚精胺(Spd)和精胺(Spm)对玉米幼苗生长、光合速率和PSⅡ光化学效率(Fv/Fm)、叶绿体结合多胺和叶片丙二醛(M DA)含量以及抗氧化酶活性的影响.结果表明,叶面喷施1 mm o l/L的Pu t、Spd和Spm可显著增加盐胁迫下玉米幼苗干物质重、叶绿体内结合态多胺的含量、叶片净光合速率和PSⅡ光化学效率(Fv/Fm),并降低了叶片中M DA含量.外源Spd和Spm明显增加盐胁迫下玉米幼苗的抗坏血酸过氧化物酶(APX)、过氧化物酶(POD)和过氧化氢酶(CAT)活性;外源Pu t可增强APX和POD活性,对CAT活性的影响不明显.这些结果表明多胺对玉米盐害的缓解作用可能是由于提高了叶绿体中结合态多胺的含量和叶片抗氧化酶的活性,从而增强了盐胁迫下的玉米光合能力.
