假单胞菌铁载体不产生突变体形成的进化机理

假单胞菌铁载体(Pvd)的产生是社会微生物学研究的一个重要模式系统:产生菌是合作者,而不产生菌是欺诈者。欺诈者可以不用付出Pvd合成的能量代价,而利用其他细菌产生的Pvd来获取生长所需的铁离子,因而处于竞争优势地位。合作与欺诈成为了当前解释自然界广泛存在的Pvd不产生菌进化形成的主要原理。本文将阐述荧光假单胞菌Pvd不产生菌形成的多条进化途径,并在此基础上剖析合作与欺诈原理的普遍适用性问题。     

脂肪酸影响草鱼肝细胞脂质蓄积状态及诱导其凋亡的离体研究

为探究外源脂肪酸对草鱼肝细胞脂质代谢及健康状况的影响及其机理,体外培养草鱼肝细胞,并采用不同浓度（0-1 mmol/L）油酸（Oleic acid）进行细胞孵育,噻唑兰比色法（Methyl thiazolte trazoliu,MTT）和油红O染色提取法检测肝细胞活力及脂质蓄积状况,BODIBY和DAPI染色法观察肝细胞脂滴及细胞核情况,流式细胞术检测肝细胞凋亡率变化,Real-time qPCR检测脂质合成标志基因过氧化物酶体增殖物激活受体γ（Peroxidase proliferation activated receptor,PPARγ）和CCAAT/增强子结合蛋白α（CCAAT/enhancer binding protein alpha,C/EBPα）、凋亡相关基因Caspase家族等的表达情况。结果显示,随着油酸处理浓度的增加,肝细胞活力和细胞内脂质积累呈现先上升后下降的趋势,分别在0.4和0.6 mmol/L时达到最大值（P < 0.05）;肝细胞凋亡率则先下降后上升,在0.4 mmol/L油酸处理时最低,1 mmol/L油酸处理时最高（P < 0.05）;此外,0.4 mmol/L油酸处理抑制了肝细胞Caspase-3b和Caspase-9基因的表达,上调Bcl-2/Bax mRNA比值（P < 0.05）,而0.8 mmol/L油酸处理显著促进Caspase-3b、Caspase-8、Caspase-9及凋亡诱导因子（Apoptosis inducing factor,AIF）基因的表达,下调Bcl-2/Bax的mRNA比值（P < 0.05）。研究表明,一定浓度的脂肪酸可增强草鱼肝细胞活力,促进胞内脂质积累,抑制细胞凋亡,而脂肪酸浓度过高则抑制肝细胞活力并诱导肝细胞凋亡,其作用与脂肪酸影响脂质代谢及凋亡基因的表达有关。     

miR-146a抑制酪氨酸酶基因家族在小鼠黑色素细胞中表达

miRNA是在许多生物过程中都起着至关重要作用的一类内源性非编码的小RNA,与癌症、肿瘤的发生有关。现发现很多miRNA在黑色素生成中都有重要的调控作用,但miR-146a是否对黑色素的生成具有影响未见报道。本研究发现miR-146a通过靶向抑制酪氨酸酶相关蛋白1(tyrosinase related protein 1,TYRP1)的表达而使黑色素生成降低。在小鼠黑色素细胞中分别转染miR-146a mimic和miR-146a 抑制剂,通过qRT-PCR与Western印迹分析比较各实验组中TYRP1基因与酪氨酸家族相关基因酪氨酸酶(tyrosinase, TYR)、酪氨酸酶相关蛋白2(tyrosinase related protein 2, TYRP2)的表达差异。双荧光报告实验验证TYRP1与miR-146a的靶向关系,双荧光酶活性结果显示,实验组相比对照组,荧光素酶活性明显降低,说明TYRP1是miR-146a的靶基因之一;qRT-PCR和Western印迹结果显示实验组TYR、TYRP1及TYRP2 在mRNA水平和蛋白质水平表达均显著降低;紫外分光光度法检测黑色素含量,结果显示miR-146a mimic转染组黑色素含量明显下降,而抑制组的黑色素含量呈上升趋势。综上所述,miR-146a通过靶向抑制TYRP1基因的表达,而影响TYR家族成员的表达,调控黑色素的生物合成。     

miR-411a-3p抑制羊驼黑色素细胞黑色素的生成

microRNA-411a-3p（miR-411a-3p）在不同毛色羊驼皮肤中差异表达,提示其可能在毛色形成中起调控作用。为证明miR-411a-3p在羊驼皮毛黑色素形成中的作用,本研究通过生物信息学预测及靶基因搜索,发现胰岛素样生长因子1受体（IGF1R）是miR-411a-3p的靶基因,继而构建了含Igf1r mRNA 3′-UTR的荧光素酶报告基因载体。报告基因转染结合报告酶活性测定证明,Igf1r是miR-411a-3p的靶基因。原位杂交显示,miR-411a-3p主要在羊驼黑色素细胞胞质中表达,提示其可能在黑色素细胞中具有重要作用。qRT-PCR揭示,棕色和黑色羊驼皮肤中miR-411a-3p表达量明显低于白色羊驼。qRT-PCR联合蛋白质印迹分析显示,在羊驼黑色素细胞过表达miR-411a-3p,伴随Igf1r下调,小眼畸形相关转录因子（Mitf）依赖的毛色基因酪氨酸酶（Tyr）、酪氨酸酶相关蛋白-2（Tyrp2）及黑色素表达水平明显下调。上述结果提示,miR-411a-3p可通过靶向抑制Igf1r负调控羊驼黑色素黑色素合成。该结果将加深我们对羊驼毛色形成机制的认识。     

Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. IV. Genetic Constraints Guide Evolutionary Trajectories in a Parallel Adaptive Radiation

The capacity for phenotypic evolution is dependent upon complex webs of functional interactions that connect genotype and phenotype. Wrinkly spreader (WS) genotypes arise repeatedly during the course of a model Pseudomonas adaptive radiation. Previous work showed that the evolution of WS variation was explained in part by spontaneous mutations in wspF, a component of the Wsp-signaling module, but also drew attention to the existence of unknown mutational causes. Here, we identify two new mutational pathways (Aws and Mws) that allow realization of the WS phenotype: in common with the Wsp module these pathways contain a di-guanylate cyclase-encoding gene subject to negative regulation. Together, mutations in the Wsp, Aws, and Mws regulatory modules account for the spectrum of WS phenotype-generating mutations found among a collection of 26 spontaneously arising WS genotypes obtained from independent adaptive radiations. Despite a large number of potential mutational pathways, the repeated discovery of mutations in a small number of loci (parallel evolution) prompted the construction of an ancestral genotype devoid of known (Wsp, Aws, and Mws) regulatory modules to see whether the types derived from this genotype could converge upon the WS phenotype via a novel route. Such types—with equivalent fitness effects—did emerge, although they took significantly longer to do so. Together our data provide an explanation for why WS evolution follows a limited number of mutational pathways and show how genetic architecture can bias the molecular variation presented to selection.UNDERSTANDING—and importantly, predicting—phenotypic evolution requires knowledge of the factors that affect the translation of mutation into phenotypic variation—the raw material of adaptive evolution. While much is known about mutation rate (e.g., Drake et al. 1998; Hudson et al. 2002), knowledge of the processes affecting the translation of DNA sequence variation into phenotypic variation is minimal.Advances in knowledge on at least two fronts suggest that progress in understanding the rules governing the generation of phenotypic variation is possible (Stern and Orgogozo 2009). The first stems from increased awareness of the genetic architecture underlying specific adaptive phenotypes and recognition of the fact that the capacity for evolutionary change is likely to be constrained by this architecture (Schlichting and Murren 2004; Hansen 2006). The second is the growing number of reports of parallel evolution (e.g., Pigeon et al. 1997; ffrench-Constant et al. 1998; Allender et al. 2003; Colosimo et al. 2004; Zhong et al. 2004; Boughman et al. 2005; Shindo et al. 2005; Kronforst et al. 2006; Woods et al. 2006; Zhang 2006; Bantinaki et al. 2007; McGregor et al. 2007; Ostrowski et al. 2008)—that is, the independent evolution of similar or identical features in two or more lineages—which suggests the possibility that evolution may follow a limited number of pathways (Schluter 1996). Indeed, giving substance to this idea are studies that show that mutations underlying parallel phenotypic evolution are nonrandomly distributed and typically clustered in homologous genes (Stern and Orgogozo 2008).While the nonrandom distribution of mutations during parallel genetic evolution may reflect constraints due to genetic architecture, some have argued that the primary cause is strong selection (e.g., Wichman et al. 1999; Woods et al. 2006). A means of disentangling the roles of population processes (selection) from genetic architecture is necessary for progress (Maynard Smith et al. 1985; Brakefield 2006); also necessary is insight into precisely how genetic architecture might bias the production of mutations presented to selection.Despite their relative simplicity, microbial populations offer opportunities to advance knowledge. The wrinkly spreader (WS) morphotype is one of many different niche specialist genotypes that emerge when experimental populations of Pseudomonas fluorescens are propagated in spatially structured microcosms (Rainey and Travisano 1998). Previous studies defined, via gene inactivation, the essential phenotypic and genetic traits that define a single WS genotype known as LSWS (Spiers et al. 2002, 2003) (Figure 1). LSWS differs from the ancestral SM genotype by a single nonsynonymous nucleotide change in wspF. Functionally (see Figure 2), WspF is a methyl esterase and negative regulator of the WspR di-guanylate cyclase (DGC) (Goymer et al. 2006) that is responsible for the biosynthesis of c-di-GMP (Malone et al. 2007), the allosteric activator of cellulose synthesis enzymes (Ross et al. 1987). The net effect of the wspF mutation is to promote physiological changes that lead to the formation of a microbial mat at the air–liquid interface of static broth microcosms (Rainey and Rainey 2003).Open in a separate windowFigure 1.—Outline of experimental strategy for elucidation of WS-generating mutations and their subsequent identity and distribution among a collection of independently evolved, spontaneously arising WS genotypes. The strategy involves, first, the genetic analysis of a specific WS genotype (e.g., LSWS) to identify the causal mutation, and second, a survey of DNA sequence variation at specific loci known to harbor causal mutations among a collection of spontaneously arising WS genotypes. For example, suppressor analysis of LSWS using a transposon to inactivate genes necessary for expression of the wrinkly morphology delivered a large number of candidate genes (top left) (Spiers et al. 2002). Genetic and functional analysis of these candidate genes (e.g., Goymer et al. 2006) led eventually to the identity of the spontaneous mutation (in wspF) responsible for the evolution of LSWS from the ancestral SM genotype (Bantinaki et al. 2007). Subsequent analysis of the wspF sequence among 26 independent WS genotypes (bottom) showed that 50% harbored spontaneous mutations (of different kinds; see Open in a separate windowFigure 2.—Network diagram of DGC-encoding pathways underpinning the evolution of the WS phenotype and their regulation. Overproduction of c-di-GMP results in overproduction of cellulose and other adhesive factors that determine the WS phenotype. The ancestral SBW25 genome contains 39 putative DGCs, each in principle capable of synthesizing the production of c-di-GMP, and yet WS genotypes arise most commonly as a consequence of mutations in just three DGC-containing pathways: Wsp, Aws, and Mws. In each instance, the causal mutations are most commonly in the negative regulatory component: wspF, awsX, and the phosphodiesterase domain of mwsR (see text).To determine whether spontaneous mutations in wspF are a common cause of the WS phenotype, the nucleotide sequence of this gene was obtained from a collection of 26 spontaneously arising WS genotypes (WS_A-Z) taken from 26 independent adaptive radiations, each founded by the same ancestral SM genotype (Figure 1): 13 contained mutations in wspF (Bantinaki et al. 2007). The existence of additional mutational pathways to WS provided the initial motivation for this study.

TABLE 1

Mutational causes of WS

Variation in transport explains polymorphism of histidine and urocanate utilization in a natural Pseudomonas population

Phenotypic variation is a fundamental requirement for evolution by natural selection. While evidence of phenotypic variation in natural populations abounds, its genetic basis is rarely understood. Here we report variation in the ability of plant-colonizing Pseudomonas to utilize histidine, and its derivative, urocanate, as sole sources of carbon and nitrogen. From a population of 164 phyllosphere-colonizing Pseudomonas strains, 77% were able to utilize both histidine and urocanate (His(+) , Uro(+) ) as growth substrates, whereas the remainder could utilize histidine, but not urocanate (His(+) , Uro(-) ), or vice versa (His(-) , Uro(+) ). An in silico analysis of the hut locus, which determines capacity to utilize both histidine and urocanate, from genome-sequenced Pseudomonas strains, showed significant variation in the number of putative transporters. To identify transporter genes specific for histidine and urocanate, we focused on a single genotype of Pseudomonas fluorescens, strain SBW25, which is capable of utilizing both substrates. Site-directed mutagenesis, combined with [(3) H]histidine transport assays, shows that hutT(u) encodes a urocanate-specific transporter; hutT(h) encodes the major high-affinity histidine transporter; and hutXWV encodes an ABC-type transporter that plays a minor role in histidine uptake. Introduction of cloned copies of hutT(h) and hutT(u) from SBW25 into strains incapable of utilizing either histidine, or urocanate, complemented the defect, demonstrating a lack of functional transporters in these strains. Taken together our data show that variation in transport systems, and not in metabolic genes, explains a naturally occurring phenotypic polymorphism.     

IGF1和IGF1R在小鼠第一个毛囊生长周期皮肤的表达

毛囊生长周期中,真皮乳头和毛基质间的基质 上皮信号调控细胞的增殖和分化。多功能细胞调控因子胰岛素样生长因子1（IGF1)是该信号路径的成员之一。第1个毛囊生长周期决定着毛囊的正常生长和发育,但IGF1在此期的作用未见报道。实时荧光定量PCR结果显示,IGF1在生长期皮肤中的相对表达量最低,在退化期表达量最高,在静止期表达量又降低。与生长初期相比,IGF1在退化期和静止期的表达量呈差异极显著（P＜0.01）;胰岛素样生长因子1受体（IGF1R）在生长期皮肤中的相对表达量最高,在退化期表达量最低,而在静止期表达量又升高。与生长初期相比,IGF1R在退化期和静止期的表达量呈差异极显著（P＜0.01）。Western 印迹结果显示,IGF1和IGF1R蛋白在小鼠皮肤第1个毛囊生长周期各阶段的表达趋势分别与其mRNA的表达趋势一致;免疫组织化学结果表明,IGF1主要分布在小鼠表皮,而IGF1R免疫阳性在小鼠毛囊毛球部、内外根鞘和毛乳头均有分布。以上实验结果揭示,IGF1和IGF1R在小鼠皮肤第1个毛囊生长周期的各阶段的差异性表达,可能在毛囊生长周期各阶段的转化过程中参与了黑色素的形成。然而,IGF1和IGF1R表达趋势不一致,提示IGF1在小鼠皮肤中发挥作用时,并非只与IGF1R结合才能发挥作用。     

MicroRNA-411a-3p靶向钙/钙调素依赖蛋白激酶4调控羊驼黑色素细胞中的黑色素生成

羊驼是重要的毛用型经济动物,具有22种天然色。毛色由皮肤中黑色素细胞产生的黑色素颗粒的分布和转运所决定的。然而,羊驼色素形成或毛色形成的分子机制复杂,由多个基因、miRNA 和lncRNA调控。但是,miR-411a-3p 对羊驼色素形成起调控作用未见报道。为研究miR-411a-3p在黑色素产生过程中的调控作用,本文将构建的miR-411a-3p载体转染到羊驼黑色素细胞中,并对毛色基因的表达进行研究。经生物信息学预测,钙/钙调素依赖蛋白激酶4(calcium-calmodulin dependent protein kinase 4, CaMK4)可能是miR-411a-3p的靶基因之一。双荧光素酶报告基因结果显示,与对照组相比,双荧光报告酶活性下降（34.78 ± 16.09）%(P<0.01),其下降趋势明显,说明CaMK4可能是miR-411a-3p的靶基因之一。miR-411a-3p通过结合CaMK4的3′ untranslated region (3′-UTR)直接调控CaMK4的表达。在羊驼黑色素细胞中转染miR-411a-3p后,CaMK4、CDK5和TYRP1在转录水平的表达量与NC组相比具有显著下降趋势,其中TYRP1下降趋势尤为显著（53.66 ± 2.11）%（P<0.01）。Western印迹检测CaMK4、CDK5、TYRP1、p-CREB在蛋白质水平的表达与NC组相比下降趋势明显,尤其是CDK5和p-CREB基因下降极为显著,分别为（70.26 ± 4.84）%（P<0.01）和（70.11 ±9.05）%（P<0.01）。Masson-Fontana法检测黑色素颗粒,结果显示,miR-411a-3p抑制黑色素细胞产生黑色素颗粒。通过紫外分光度法检测真黑素（eumelanin,EM）和褐黑素（phenomelanin,PM）显示,EM和PM的含量均被下调。结果表明,miR-411a-3p靶向抑制CaMK4表达,从而改变CREB的表达以控制黑色素的产生,此研究结果对哺乳动物毛色形成机制有重要意义。