Common evolutionary origin of the central portions of the Ri TL-DNA of Agrobacterium rhizogenes and the Ti T-DNAs of Agrobacterium tumefaciens

Analysis of published sequences for Ri TL-DNA (root-inducing left-hand transferred DNA) of Agrobacterium rhizogenes revealed several unsuspected structural features. First, Ri TL-DNA genes are redundant. Using redundancy as a criterion, three regions (left, middle and right) were discerned. The left one, ORFs (open reading frames) 1–7, contains no detectable redundancy. In the middle region a highly diverged gene family was detected in ORFs 8, 11, 12, 13 and 14. The right region contains an apparently recent duplication (ORF 15 =18+17). We interpret the phenomenon of redundancy, particularly in the central region that encodes the transformed phenotype, to be an adaptation that ensures function in a variety of host species. Comparison of Ri TL-DNA and Ti T-DNAs from Agrobacterium tumefaciens revealed common structures, unpredicted by previous nucleic acid hybridization studies. Ri TL-DNA ORF 8 is a diverged Ti T-DNA tms1. Both Agrobacterium genes consist of a member of the diverged gene family detected in the central part of the Ri TL-DNA, but fused to a sequence similar to iaaM of Pseudomonas savastonoi. Other members of this gene family were found scattered throughout Ti T-DNA. We argue that the central region of Ri and the part of Ti T-DNA including ORFs 5–10 evolved from a common ancestor. We present the hypothesis that the gene family encodes functions that alter developmental plasticity in higher plants.     

Domestication of the Emblematic White Cheese-Making Fungus Penicillium camemberti and Its Diversification into Two Varieties

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明适应条件下鲤属鱼L-型外水平细胞反应的给光-瞬变成分

在明适应条件下鲤属鱼 L-型外水平细胞的反应显示明显的给光-瞬变成分(on-transient)、它与刺激波长有关——对蓝、绿光的反应比对红光的反应有更明显的瞬变成分,其光谱特性提示它与绿敏锥细胞的输入信号有关。与已报道的其它动物 L 型水平细胞的给光-瞬变成分不同,它的出现在一定范围内与网膜受照射的面积无关。绿色(502nm)和红色(706nm)闪光同时照射所引起反应的给光-瞬变成分比各自单独刺激时要显著得多,提示它也与绿敏锥细胞和红敏锥细胞输入的相互作用有关。     

The evolution of male-female dimorphism: Older than sex?

This contribution considers the evolution of a dimorphism with respect to cell fusion characteristics in a population of primitive cells. These cells reproduce exclusively asexually. The evolution towards asymmetric fusion behaviour of cells is driven by selection promoting horizontal transfer of an endosymbiontic replicator. It is concluded that evolution of asymmetric cell fusion in this scenario is more likely than evolution of sexual differentiation in a sexually reproducing population. Pre-existing dimorphism with respect to cell fusion may thus have been the basis for the establishment of sexual differentiation at the level of gamete fusion, and this in turn is fundamental to the evolution of two different sexes, male and female.     

On the evolution of protamines in bony Fish: Alternatives to the “Retroviral horizontal transmission” hypothesis

Fish protamines are highly specialized molecules which are responsible for chromatin condensation during the last stages of spermatogenesis (spermiogenesis). However, not all fish contain protamines in their sperm nuclei; rather, there seems to be a random distribution of protamines within this group. The origin of this sporadic presence of protamines in the sperm and its significance have not yet been precisely determined. In this paper we have conducted an exhaustive survey of the literature available on the different types of nuclear protein composition of the sperm of teleost fish in order to try to correlate these data with what is presently known about the taxonomy of this group. The results of this analysis have allowed us to make the following observations. The divergence between protamines and histones has occurred several times during the evolution of the bony fish. However, the relative frequency of this divergence is almost negligible during the differentiation of genera and species (intrafamily variation) and is very small during the differentiation of families (interfamily variation). Nevertheless, the divergence is very noticeable among the different orders. It is therefore possible to conclude from all this that the sporadic distribution of protamines in bony fish is not a random event as initially believed. Furthermore, such a heterogeneous distribution of protamines cannot be easily accounted for by a mechanism of horizontal retroviral transmission through repeated and independent acquisition of a prot amine gene as has been recently proposed (Jankowski, Stater, Dixon (1986) J Mol Evol 23:1–10). Rather, it could possibly be explained by a repeated and independent loss of the expression of the protamine gene (or loss of the gene itself) which mainly occurred during the diversification of the orders of this group.Correspondence to: J. Ausio     

Experimental and computational analysis of the ancestry of an evolutionary young enzyme from histidine biosynthesis

The conservation of fold and chemistry of the enzymes associated with histidine biosynthesis suggests that this pathway evolved prior to the diversification of Bacteria, Archaea, and Eukaryotes. The only exception is the histidinol phosphate phosphatase (HolPase). So far, non-homologous HolPases that possess distinct folds and belong to three different protein superfamilies have been identified in various phylogenetic clades. However, their evolution has remained unknown to date. Here, we analyzed the evolutionary history of the HolPase from γ-Proteobacteria (HisB-N). It has been argued that HisB-N and its closest homologue d -glycero-d -manno-heptose-1,7-bisphosphate 7-phosphatase (GmhB) have emerged from the same promiscuous ancestral phosphatase. GmhB variants catalyze the hydrolysis of the anomeric d -glycero-d -manno-heptose-1,7-bisphosphate (αHBP or βHBP) with a strong preference for one anomer (αGmhB or βGmhB). We found that HisB-N from Escherichia coli shows promiscuous activity for βHBP but not αHBP, while βGmhB from Crassaminicella sp. shows promiscuous activity for HolP. Accordingly, a combined phylogenetic tree of αGmhBs, βGmhBs, and HisB-N sequences revealed that HisB-Ns form a compact subcluster derived from βGmhBs. Ancestral sequence reconstruction and in vitro analysis revealed a promiscuous HolPase activity in the resurrected enzymes prior to functional divergence of the successors. The following increase in catalytic efficiency of the HolP turnover is reflected in the shape and electrostatics of the active site predicted by AlphaFold. An analysis of the phylogenetic tree led to a revised evolutionary model that proposes the horizontal gene transfer of a promiscuous βGmhB from δ- to γ-Proteobacteria where it evolved to the modern HisB-N.     

The ecology of the calanoid copepod Eurytemora affinis in salt marsh tide pools

We describe selected aspects of the ecology of the copepod Eurytemora affinis in tide pools of an inland salt marsh near L'Isle-Verte, Québec along the southern shore of the St. Lawrence estuary. E. affinis performed daily horizontal migrations moving from the centers of pools to the banks and into dense algae. Male E. affinis were mainly found in the center of the pools during twilight (21 : 00 hrs) and in dense algae in daylight (12: 00 hrs) whereas most females and copepodites were found near the banks at all three sampling periods. Although these daily movements among sites may have minimized predation by diurnally foraging sticklebacks (Pisces: Gasterosteidae), other explanations for the movements can not be excluded. We also quantified the effects of fish predation upon the population structure of E. affinis. Densities of all stages (nauplius, copepodite, adult) were significantly lower in pools with fish than in pools without fish. Female E. affinis were significantly smaller (mean length) in pools with fish than in pools without fish, indicating that the sticklebacks selectively ate larger females. Male-biased sex ratios were found in both types of pools, which excluded the possibility that biased ratios in this species are caused by selective predation upon the females.