Brca2 is involved in meiosis in Arabidopsis thaliana as suggested by its interaction with Dmc1

Two BRCA2-like sequences are present in the Arabidopsis genome. Both genes are expressed in flower buds and encode nearly identical proteins, which contain four BRC motifs. In a yeast two-hybrid assay, the Arabidopsis Brca2 proteins interact with Rad51 and Dmc1. RNAi constructs aimed at silencing the BRCA2 genes at meiosis triggered a reproducible sterility phenotype, which was associated with dramatic meiosis alterations. We obtained the same phenotype upon introduction of RNAi constructs aimed at silencing the RAD51 gene at meiosis in dmc1 mutant plants. The meiotic figures we observed strongly suggest that homologous recombination is highly disturbed in these meiotic cells, leaving aberrant recombination events to repair the meiotic double-strand breaks. The 'brca2' meiotic phenotype was eliminated in spo11 mutant plants. Our experiments point to an essential role of Brca2 at meiosis in Arabidopsis. We also propose a role for Rad51 in the dmc1 context.

Comparative analysis of genome maintenance genes in naked mole rat, mouse, and human

Genome maintenance (GM) is an essential defense system against aging and cancer, as both are characterized by increased genome instability. Here, we compared the copy number variation and mutation rate of 518 GM-associated genes in the naked mole rat (NMR), mouse, and human genomes. GM genes appeared to be strongly conserved, with copy number variation in only four genes. Interestingly, we found NMR to have a higher copy number of CEBPG, a regulator of DNA repair, and TINF2, a protector of telomere integrity. NMR, as well as human, was also found to have a lower rate of germline nucleotide substitution than the mouse. Together, the data suggest that the long-lived NMR, as well as human, has more robust GM than mouse and identifies new targets for the analysis of the exceptional longevity of the NMR.

Comparative analysis and distribution of Omega-3 lcPUFA Biosynthesis genes in marine molluscs

Recent research has identified marine molluscs as an excellent source of omega-3 long-chain polyunsaturated fatty acids (lcPUFAs), based on their potential for endogenous synthesis of lcPUFAs. In this study we generated a representative list of fatty acyl desaturase (Fad) and elongation of very long-chain fatty acid (Elovl) genes from major orders of Phylum Mollusca, through the interrogation of transcriptome and genome sequences, and various publicly available databases. We have identified novel and uncharacterised Fad and Elovl sequences in the following species: Anadara trapezia, Nerita albicilla, Nerita melanotragus, Crassostrea gigas, Lottia gigantea, Aplysia californica, Loligo pealeii and Chlamys farreri. Based on alignments of translated protein sequences of Fad and Elovl genes, the haeme binding motif and histidine boxes of Fad proteins, and the histidine box and seventeen important amino acids in Elovl proteins, were highly conserved. Phylogenetic analysis of aligned reference sequences was used to reconstruct the evolutionary relationships for Fad and Elovl genes separately. Multiple, well resolved clades for both the Fad and Elovl sequences were observed, suggesting that repeated rounds of gene duplication best explain the distribution of Fad and Elovl proteins across the major orders of molluscs. For Elovl sequences, one clade contained the functionally characterised Elovl5 proteins, while another clade contained proteins hypothesised to have Elovl4 function. Additional well resolved clades consisted only of uncharacterised Elovl sequences. One clade from the Fad phylogeny contained only uncharacterised proteins, while the other clade contained functionally characterised delta-5 desaturase proteins. The discovery of an uncharacterised Fad clade is particularly interesting as these divergent proteins may have novel functions. Overall, this paper presents a number of novel Fad and Elovl genes suggesting that many mollusc groups possess most of the required enzymes for the synthesis of lcPUFAs.

Structure and vascular tissue expression of duplicated TERMINAL EAR1-like paralogues in poplar

TERMINAL EAR1-like (TEL) genes encode putative RNA-binding proteins only found in land plants. Previous studies suggested that they may regulate tissue and organ initiation in Poaceae. Two TEL genes were identified in both Populus trichocarpa and the hybrid aspen Populus tremula × P. alba, named, respectively, PoptrTEL1-2 and PtaTEL1-2. The analysis of the organisation around the PoptrTEL genes in the P. trichocarpa genome and the estimation of the synonymous substitution rate for PtaTEL1-2 genes indicate that the paralogous link between these two Populus TEL genes probably results from the Salicoid large-scale gene-duplication event. Phylogenetic analyses confirmed their orthology link with the other TEL genes. The expression pattern of both PtaTEL genes appeared to be restricted to the mother cells of the plant body: leaf founder cells, leaf primordia, axillary buds and root differentiating tissues, as well as to mother cells of vascular tissues. Most interestingly, PtaTEL1-2 transcripts were found in differentiating cells of secondary xylem and phloem, but probably not in the cambium itself. Taken together, these results indicate specific expression of the TEL genes in differentiating cells controlling tissue and organ development in Populus (and other Angiosperm species).

Validation of in silico-predicted genic SNPs in white clover (Trifolium repens L.), an outbreeding allopolyploid species

White clover (Trifolium repens L.) is an obligate outbreeding allotetraploid forage legume. Gene-associated SNPs provide the optimum genetic system for improvement of such crop species. An EST resource obtained from multiple cDNA libraries constructed from numerous genotypes of a single cultivar has been used for in silico SNP discovery and validation. A total of 58 from 236 selected sequence clusters (24.5%) were fully validated as containing polymorphic SNPs by genotypic analysis across the parents and progeny of several two-way pseudo-testcross mapping families. The clusters include genes belonging to a broad range of predicted functional categories. Polymorphic SNP-containing ESTs have also been used for comparative genomic analysis by comparison with whole genome data from model legume species, as well as Arabidopsis thaliana. A total of 29 (50%) of the 58 clusters detected putative ortholoci with known chromosomal locations in Medicago truncatula, which is closely related to white clover within the Trifolieae tribe of the Fabaceae. This analysis provides access to translational data from model species. The efficiency of in silico SNP discovery in white clover is limited by paralogous and homoeologous gene duplication effects, which are resolved unambiguously by the transmission test. This approach will also be applicable to other agronomically important cross-pollinating allopolyploid plant species.

Analysis of the amino acid sequences of plant Bowman-Birk inhibitors

Plant seeds contain a large number of protease inhibitors of animal, fungal, and bacterial origin. One of the well-studied families of these inhibitors is the Bowman-Birk family(BBI). The BBIs from dicotyledonous seeds are 8K, double-headed proteins. In contrast, the 8K inhibitors from monocotyledonous seeds are single headed. Monocots also have a 16K, double-headed inhibitor. We have determined the primary structure of a Bowman-Birk inhibitor from a dicot, horsegram, by sequential edman analysis of the intact protein and peptides derived from enzymatic and chemical cleavage. The 76-residue-long inhibitor is very similar to that ofMacrotyloma axillare. An analysis of this inhibitor along with 26 other Bowman-Birk inhibitor domains (MW 8K) available in the SWISSPROT databank revealed that the proteins from monocots and dicots belong to related but distinct families. Inhibitors from monocots show larger variation in sequence. Sequence comparison shows that a crucial disulphide which connects the amino and carboxy termini of the active site loop is lost in monocots. The loss of a reactive site in monocots seems to be correlated to this. However, it appears that this disulphide is not absolutely essential for retention of inhibitory function. Our analysis suggests that gene duplication leading to a 16K inhibitor in monocots has occurred, probably after the divergence of monocots and dicots, and also after the loss of second reactive site in monocots.

Evolution of sequence specificity in a restriction endonuclease by a point mutation

Restriction endonucleases (REases) protect bacteria from invading foreign DNAs and are endowed with exquisite sequence specificity. REases have originated from the ancestral proteins and evolved new sequence specificities by genetic recombination, gene duplication, replication slippage, and transpositional events. They are also speculated to have evolved from nonspecific endonucleases, attaining a high degree of sequence specificity through point mutations. We describe here an example of generation of exquisitely site-specific REase from a highly-promiscuous one by a single point mutation.

The primary structure of sheep liver cytosolic serine hydroxymethyltransferase and an analysis of the evolutionary relationships among serine hydroxymethyltransferases

The complete amino-acid sequence of sheep liver cytosolic serine hydroxymethyltransferase was determined from an analysis of tryptic, chymotryptic, CNBr and hydroxylamine peptides. Each subunit of sheep liver serine hydroxymethyltransferase consisted of 483 amino-acid residues. A comparison of this sequence with 8 other serine hydroxymethyltransferases revealed that a possible gene duplication event could have occurred after the divergence of animals and fungi. This analysis also showed independent duplication of SHMT genes in Neurospora crassa. At the secondary structural level, all the serine hydroxymethyltransferases belong to the alpha/beta category of proteins. The predicted secondary structure of sheep liver serine hydroxymethyltransferase was similar to that of the observed structure of tryptophan synthase, another pyridoxal 5'-phosphate containing enzyme, suggesting that sheep liver serine hydroxymethyltransferase might have a similar pyridoxal 5'-phosphate binding domain. In addition, a conserved glycine rich region, G L Q G G P, was identified in all the serine hydroxymethyltransferases and could be important in pyridoxal 5'-phosphate binding. A comparison of the cytosolic serine hydroxymethyltransferases from rabbit and sheep liver with other proteins sequenced from both these sources showed that serine hydroxymethyltransferase was a highly conserved protein. It was slightly less conserved than cytochrome c but better conserved than myoglobin, both of which are well known evolutionary markers. C67 and C203 were specifically protected by pyridoxal 5'-phosphate against modification with [C-14]iodoacetic acid, while C247 and C261 were buried in the native serine hydroxymethyltransferase. However, the cysteines are not conserved among the various serine hydroxymethyltransferases. The exact role of the cysteines in the reaction catalyzed by serine hydroxymethyltransferase remains to be elucidated.

Bi-Domain Protein Tyrosine Phosphatases Reveal an Evolutionary Adaptation to Optimize Signal Transduction

Significance: The bi-domain protein tyrosine phosphatases (PTPs) exemplify functional evolution in signaling proteins for optimal spatiotemporal signal transduction. Bi-domain PTPs are products of gene duplication. The catalytic activity, however, is often localized to one PTP domain. The inactive PTP domain adopts multiple functional roles. These include modulation of catalytic activity, substrate specificity, and stability of the bi-domain enzyme. In some cases, the inactive PTP domain is a receptor for redox stimuli. Since multiple bi-domain PTPs are concurrently active in related cellular pathways, a stringent regulatory mechanism and selective cross-talk is essential to ensure fidelity in signal transduction. Recent Advances: The inactive PTP domain is an activator for the catalytic PTP domain in some cases, whereas it reduces catalytic activity in other bi-domain PTPs. The relative orientation of the two domains provides a conformational rationale for this regulatory mechanism. Recent structural and biochemical data reveal that these PTP domains participate in substrate recruitment. The inactive PTP domain has also been demonstrated to undergo substantial conformational rearrangement and oligomerization under oxidative stress. Critical Issues and Future Directions: The role of the inactive PTP domain in coupling environmental stimuli with catalytic activity needs to be further examined. Another aspect that merits attention is the role of this domain in substrate recruitment. These aspects have been poorly characterized in vivo. These lacunae currently restrict our understanding of neo-functionalization of the inactive PTP domain in the bi-domain enzyme. It appears likely that more data from these research themes could form the basis for understanding the fidelity in intracellular signal transduction.

Paralogous cAMP Receptor Proteins in Mycobacterium smegmatis Show Biochemical and Functional Divergence

The cyclic AMP receptor protein (CRP) family of transcription factors consists of global regulators of bacterial gene expression. Here, we identify two paralogous CRPs in the genome of Mycobacterium smegmatis that have 78% identical sequences and characterize them biochemically and functionally. The two proteins (MSMEG_0539 and MSMEG_6189) show differences in cAMP binding affinity, trypsin sensitivity, and binding to a CRP site that we have identified upstream of the msmeg_3781 gene. MSMEG_6189 binds to the CRP site readily in the absence of cAMP, while MSMEG_0539 binds in the presence of cAMP, albeit weakly. msmeg_6189 appears to be an essential gene, while the ?msmeg_0539 strain was readily obtained. Using promoter-reporter constructs, we show that msmeg_3781 is regulated by CRP binding, and its transcription is repressed by MSMEG_6189. Our results are the first to characterize two paralogous and functional CRPs in a single bacterial genome. This gene duplication event has subsequently led to the evolution of two proteins whose biochemical differences translate to differential gene regulation, thus catering to the specific needs of the organism.

三叶木通花发育相关基因的结构、功能和进化研究

花是被子植物最关键的创新（innovation）性状。在被子植物的不同类群中，其形态多种多样，尤其以基部真双子叶植物的花形态最为丰富。大量的系统发育分析表明，在核心真双子叶植物起源之前，几个与花发育相关的MADS-box基因亚家族均发生了大尺度的基因重复事件。因此，在被子植物的不同物种中，花发育相关基因的组成并不相同，并且它们经历了不同的进化历史，这意味着这些基因可能以不同的方式调控花的发育。基部真双子叶植物，作为基部被子植物和核心真双子叶植物之间的过渡类群，对于我们理解被子植物花的进化，揭示核心真双子叶植物花的起源以及基部真双子叶植物花多样性分化的分子机制非常重要。本文以基部真双子叶植物三叶木通为研究材料，着重进行了以下研究工作： 1. 花器官发生过程的观察。三叶木通的花为雌雄同序的单性花。而且，根据成熟花的形态，三叶木通的雌花和雄花都只有一轮花被器官，即三个花瓣状的萼片。扫描电镜的观察结果表明：1）在花器官的发生和发育过程中，在萼片和雄蕊原基之间，确实没有花瓣原基或另一轮萼片原基发生。2）雌花和雄花都是以两性花的方式发生发育的。3）单性花是由于在花发育的最后阶段，雌花中雄蕊或者雄花中心皮的退化而产生的。 2. 花发育相关基因的克隆。应用5’/3’ RACE的方法，我们从三叶木通不同发育阶段的混合花芽中共分离到九个与花发育相关的MADS-box基因： AktFL1、AktFL2、AktAP3_1、AktAP3_2、AktAP3_3、AktPI、AktAG1、AktAG2和AktSEP3。 3. A类MADS-box基因的进化。由于A类基因在进化过程中序列结构的改变，再加上取样的限制，使得A类基因间的进化历史一直不能被很好的理解。因此，本文对A类基因的研究从构建该基因亚家族的系统发育树开始。主要结果如下：1）通过扩大在基部真双子叶植物和被子植物其它重要类群的取样，我们的系统发育树基本上反映了现存被子植物的系统发育关系。2）核心真双子叶植物的A类基因由三个分支组成：euFUL、euAP1和AGL79，它们是通过发生在核心真双子叶植物起源之前的两次几乎同时的基因重复事件产生的。3）在基部真双子叶植物中，山龙眼目、毛茛目和黄杨科的A类基因各形成一支。而且，在这些类群内，发生了多次小尺度的独立的基因重复事件。4）来自单子叶植物的FUL-like基因明显地构成一个单系，并且包括三个分支：OsAMDS14、OsMADS15和OsMADS18。它们是由于两次不连续的基因重复事件产生的。5）不同类型的A类基因产物在C末端拥有不同的保守基元。6）从基因组结构上看，所有的A类基因都拥有八个外显子和七个内含子。7）通过对三叶木通中两个FUL-like型基因（AktFL1和AktFL2）表达式样的观察，我们发现它们在叶原基和发育早期的花原基以及发育着的花器官中都有表达。此外，A类基因表达式样的进化分析结果表明被子植物中该类基因的祖先可能具有广泛的功能，既在营养器官中表达又在生殖器官中表达 。 4. B类基因表达式样的保守性和多样性。通过对B类基因的系统发育和表达式样分析，得到以下结果：1）三叶木通中的三个paleoAP3基因是通过两次基因重复事件产生的。2）在木通科或木通属内，PI型基因并没有发生基因重复事件。3）RT-PCR结果表明，AktAP3_1在雌花中的表达量比雄花中高，而AktAP3_2则在雄花中的表达量比雌花中高。AktAP3_3和AktPI在雌花和雄花中的表达水平相似。4）原位杂交分析显示这些基因在发育着的雄蕊和心皮中表达。此外，AktAP3_3和AktPI还在萼片中表达，可能参与花瓣状萼片的发育。 5. 三叶木通C/D和E类基因的序列结构和表达分析。通过序列结构分析，我们发现，与其它被子植物AG同源基因编码的MADS-domain蛋白一样，AktAG1和AktAG2在MADS结构域的N末端都拥有一段氨基酸序列的延伸，AktAG1为20个氨基酸;AktAG2为7个氨基酸。原位杂交分析表明AktAG1和AktAG2主要在发育着的雄蕊和心皮中表达，说明它们具有决定生殖器官发育这一保守的功能。 AktSEP3属于AGL9型的E类基因。该基因在所有花器官中都有表达，说明和其它被子植物的E类基因一样，AktSEP3在三叶木通中对于所有花器官的发育都是必需的。 6. 各类MADS-domain蛋白间的相互作用。在前面工作的基础上，我们首次对三叶木通中上述MADS-domain蛋白间的作用方式进行了研究。酵母双杂交结果表明：1）AktSEP3的C末端具有转录激活功能。2）三个AktAP3蛋白与AktPI蛋白都能够形成异源二聚体，但是它们之间的作用能力并不相同。3）AktSEP3蛋白可以与AktFL1、AktPI、AktAG1和AktAG2形成异源二聚体，充分体现了E类基因产物作用式样的保守性。4）AktFL1与AktPI、AktSEP3和AktAG2也能形成异源二聚体，这与核心真双子叶植物的euFUL型蛋白在作用式样上是非常相似的。 综合以上结果，我们探讨了三叶木通花发育的分子机制。在三叶木通的三轮花器官中，与拟南芥等模式植物相似的是：E类（AktSEP3）基因在每一轮花器官中都起作用;此外，A类（AktFL1）和B类（AktAP3_3和AktPI）基因在花瓣状的萼片中有不同程度的表达，类似于拟南芥的第二轮;B类（AktAP3_1、AktAP3_2、AktAP3_3和AktPI）和C/D类（AktAG1和AktAG2）基因在雄蕊的发育过程中起作用;C/D类（AktAG1和AktAG2）基因对心皮的发育起作用。与拟 南芥等模式植物不同的是：1）虽然原位杂交分析表明，AktFL1、AktAP3_3、AktPI和AktSEP3都在花瓣状的萼片中有 不同程度的表达，但是它们的蛋白质产物AktFL1与AktSEP3和AktAP3_3与AktPI都只能形成较弱的异源二聚体。而 且，根据我们的研究结果，在三叶木通中没有找到euAP1型的A类基因，只有两个FUL-like型的A类基因。它们的功能 与核心真双子叶植物中的euFUL型基因相似。因此，AktFL1很可能与其它调控因子共同作用负责花分生组织的形成;AktFL1/AktAG2则可能在花发育的后期起作用。那么，三叶木通花瓣状萼片的发育是否需要AktFL1/AktSEP3和 AktAP3_3/AktPI的参与，还是另有其它转录因子的参与，仍然需要更深入的研究。2）虽然在三叶木通中，雄蕊的发 育同样需要B、C/D和E类基因的参与，但是由于小尺度的基因重复事件，在该物种中只拥有三个paleoAP3型基因，而没有euAP3型基因。而且，由于复制拷贝间的亚功能化，AktAP3_1/AktPI主要参与雌花的发育过程;而AktAP3_2/AktPI主要参与雄花的发育过程。

水稻中一个编码富含脯氨酸蛋白基因家族的表达和功能研究

OsPRP1是水稻中特有的，编码一类富含脯氨酸蛋白（proline-rich protein, PRP）的基因家族，该家族有4个成员。在GenBank中，仅找到了一个结构相对接近的玉米PRP蛋白，但是对它的研究仅限于序列上的某些描述，而且在序列上，仍然与这4个OsPRP1蛋白有明显的差别。OsPRP1蛋白明显有别于前人（1999）所描述的4类PRP蛋白。它们是植物中一类新的小分子量的PRP蛋白，仅有一个保守结构域而属于DUF1210蛋白超家族的成员。 四个OsPRP1基因在基因组中紧密串联排列，而且编码区高度保守，基因结构也高度一致，证明它们来源于同一个祖先基因，是通过基因复制的方式产生的。PAML分析也证明它们在进化时间上的相互距离并不远。而在进化过程中由于执行生理功能上的某种重要性，在编码区表现出很的保守性，因而很难在RNA水平和蛋白水平上研究四个OsPRP1基因的表达差异。但是它们在表达调节区（如启动子区）显示出明显的差异。在克隆启动子的基础上，用GUS报告基因的策略，没有检测到它们在拟南芥中的表达活性，说明它们具有一定的种属特异性。而在水稻中，这四个基因的表达显示出了明显的时序和空间差异，既表现出在组织器官及其发育阶段上的特异性和变化，又在一定程度上表现出交叉，出现了功能上的分化和重叠。根据启动子区上的顺式元件，检测了这些基因对6种植物生长调节物质和3种非生物胁迫因子的应答反应，证明它们的表达调节也表现出显著的差异和分化。因此，四个基因的进化出现了功能退化、亚功能化和产生新功能等多种命运，比理论模型预期的要复杂得多，可能在执行生理功能和对环境反应上具有各自的生物学意义。 植物细胞壁是多种碳水化合物和蛋白质相互交织在一起的亲水性网络。在保护和支撑原生质、细胞通信、细胞分化、细胞对生物的和非生物胁迫的抗性等方面发挥着重要作用。目前已知的大多数植物PRP蛋白被描述成细胞壁结构性蛋白。OsPRP1基因家族编码的蛋白质都有一个N-端信号肽，暗示它们可能是一类分泌蛋白。我们用OsPRP1.1::GFP融合蛋白进行了亚细胞定位，证明了OsPRP1蛋白的确也是细胞壁相关蛋白。用原核表达体系表达了GST-融合蛋白，制备抗体，通过免疫印迹证明这些蛋白不溶于温和的提取缓冲溶液中，但可以被高盐和强碱溶液溶解，且分子量增加了三倍。证明在体内可能出现修饰、与细胞壁其它组分相交联的现象。 在这四个基因中，只有OsPRP1.2能够在水稻根中特异表达。根的原位杂交实验证明，OsPRP1在分化成熟程度低的细胞中大量表达，而在分化成熟程度高的细胞中几乎不表达。GUS染色的结果同样发现，基因在维管柱特别是中柱鞘附近的薄壁细胞的表达比别的细胞要强得多，而且在根的生长方向上表现出与发育相关的表达特征。说明OsPRP1基因可能参与了这些细胞的分化、发育过程。而基因表达的组织器官特异性的差异和对不同刺激因素的不同反应意味着它们可能参与了多种生理过程。为此构建了一个RNAi的表达载体，转化水稻，Southern杂交实验得到9个单位点插入的T2代独立株系，其中有6个株系与野生型对照相比，主根的早期伸长受到显著抑制，主根的一级侧根地数量减少，根尖分生区的细胞在轴向上的伸长受到了抑制。结合表达定位和原位杂交的结果，我们对它们在植物生长发育中的功能进行了深入探讨。

Pseudogenization of the tumor-growth promoter angiogenin in a leaf-eating monkey

Physiological functions of human genes may be studied by gene-knockout experiments in model organisms such as the mouse. This strategy relies on the existence of one-to-one gene orthology between the human and mouse. When lineage-specific gene duplication occurs and paralogous genes share a certain degree of functional redundancy, knockout mice may not provide accurate functional information on human genes. Angiogenin is a small protein that stimulates blood-vessel growth and promotes tumor development. Humans and related primates only have one angiogenin gene, while mice have three paralogous genes. This makes it difficult to generate angiogenin-knockout mice and even more difficult to interpret the genotype-phenotype relation from such animals should they be generated. We here show that in the douc langur (Pygathrix nemaeus), an Asian leaf-eating colobine monkey, the single-copy angiogenin gene has a one-nucleotide deletion in the sixth codon of the mature peptide, generating a premature stop codon. This nucleotide deletion is found in five unrelated individuals sequenced, and therefore is likely to have been fixed in the species. Five colobine species that are closely related to the douc langur have intact angiogenin genes, suggesting that the pseudogenization event was recent and unique to the douc langur lineage. This natural knockout experiment suggests that primate angiogenin is dispensable even in the wild. Further physiological studies of douc largurs may offer additional information on the role of this cancer-related gene in normal physiology of primates, including humans. Our findings also provide a strong case for the importance of evolutionary analysis in biomedical studies of gene functions. (C) 2003 Elsevier Science B.V. All rights reserved.

Adaptive diversification of bitter taste receptor genes in mammalian evolution

The diversity and evolution of bitter taste perception in mammals is not well understood. Recent discoveries of bitter taste receptor (T2R) genes provide an opportunity for a genetic approach to this question. We here report the identification of 10 and 30 putative T2R genes from the draft human and mouse genome sequences, respectively, in addition to the 23 and 6 previously known T2R genes from the two species. A phylogenetic analysis of the T2R genes suggests that they can be classified into three main groups, which are designated A, B, and C. Interestingly, while the one-to-one gene orthology between the human and mouse is common to group B and C genes, group A genes show a pattern of species- or lineage-specific duplication. It is possible that group B and C genes are necessary for detecting bitter tastants common to both humans and mice, whereas group A genes are used for species-specific bitter tastants. The analysis also reveals that phylogenetically closely related T2R genes are close in their chromosomal locations, demonstrating tandem gene duplication as the primary source of new T2Rs. For closely related paralogous genes, a rate of nonsynonymous nucleotide substitution significantly higher than the rate of synonymous substitution was observed in the extracellular regions of T2Rs, which are presumably involved in tastant-binding. This suggests the role of positive selection in the diversification of newly duplicated T2R genes. Because many natural poisonous substances are bitter, we conjecture that the mammalian T2R genes are under diversifying selection for the ability to recognize a diverse array of poisons that the organisms may encounter in exploring new habitats and diets.

Evolution of phenylalanyl-tRNA synthetase by domain losing

The gene duplication, fusion and horizontal transfer are the frequent events during evolution of many proteins, including the aminoacyl-tRNA synthetases (AARSs). However, in this work, it was shown that the main event during evolution of phenylalanyl-tRNA synthetase (PheRS) is a domain loss, and the function/activity of PheRS is not affected by domain losing. Generally, the size of genome and number of genes are increased during evolution from bacteria to eukaryote, but the interesting thing is that the type and number of PheRS domains in eukaryotae are obviously less than those in bacteria. The evolution of PheRS by domain losing seems to be related to the functional evolution of some AARSs from the multiple specificities to the single specificity.