Phylogeny and Molecular Evolution of the Green Algae

The green lineage (Viridiplantae) comprises the green algae and their descendants the land plants, and is one of the major groups of oxygenic photosynthetic eukaryotes. Current hypotheses posit the early divergence of two discrete clades from an ancestral green flagellate. One clade, the Chlorophyta, comprises the early diverging prasinophytes, which gave rise to the core chlorophytes. The other clade, the Streptophyta, includes the charophyte green algae from which the land plants evolved. Multi-marker and genome scale phylogenetic studies have greatly improved our understanding of broad-scale relationships of the green lineage, yet many questions persist, including the branching orders of the prasinophyte lineages, the relationships among core chlorophyte clades (Chlorodendrophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae), and the relationships among the streptophytes. Current phylogenetic hypotheses provide an evolutionary framework for molecular evolutionary studies and comparative genomics. This review summarizes our current understanding of organelle genome evolution in the green algae, genomic insights into the ecology of oceanic picoplanktonic prasinophytes, molecular mechanisms underlying the evolution of complexity in volvocine green algae, and the evolution of genetic codes and the translational apparatus in green seaweeds. Finally, we discuss molecular evolution in the streptophyte lineage, emphasizing the genetic facilitation of land plant origins.     

高等植物光敏色素的分子结构、生理功能和进化特征

光敏色素是植物感受外界环境变化的最重要光受体之一,对红光和远红外光非常敏感。本文综述了光敏色素的分子结构、它所包含的结构域和相应功能以及植物各主要类群中光敏色素基因家族的成员组成与进化关系;重点在分子水平上介绍了光敏色素的生理功能与作用机制。最后,基于最新的研究进展提出了将来的研究方向。     

Evolution of the Inner Light-Harvesting Antenna Protein Family of Cyanobacteria,Algae, and Plants

Two hypotheses account for the evolution of the inner antenna light-harvesting proteins of oxygenic photosynthesis in cyanobacteria, algae, and plants: one in which the CP43 protein of photosytem II gave rise to the extrinsic CP43-like antennas of cyanobacteria (i.e. IsiA and Pcb proteins), as a late development, and the other in which CP43 and CP43-like proteins derive from an ancestral protein. In order to determine which of these hypotheses is most likely, we analyzed the family of antenna proteins by a variety of phylogenetic techniques, using alignments of the six common membrane-spanning helices, constructed using information on the antenna proteins’ three-dimensional structure, and surveyed for evidence of factors that might confound inference of a correct phylogeny. The first hypothesis was strongly supported. As a consequence, we conclude that the ancestral photosynthetic apparatus, with 11 membrane-spanning helices, split at an early stage during evolution to form, on the one hand, the reaction center of photosystem II and, on the other hand, the ancestor of inner antenna proteins, CP43 (PsbC) and CP47 (PsbB). Only much later in evolution did the CP43 lineage give rise to the CP43’ proteins (IsiA and Pcb) of cyanobacteria. [Reviewing Editor: Dr. Patrick Keeling]     

新型冠状病毒PLpro蛋白酶结构与功能的生物信息学分析

2019年12月,由新型冠状病毒(SARS-CoV-2)引起的新型冠状病毒肺炎(COVID-19)在中国武汉暴发。SARS-CoV-2的基因组编码2种病毒蛋白酶,即木瓜样蛋白酶(Papain-like protease,PLpro)和3C样蛋白酶(3C-like protease)。其中PLpro是SARS-CoV-2复制酶复合体(RC)形成的重要调节蛋白分子,对于病毒基因组转录和复制至关重要。因此,将SARS-CoV-2 PLpro作为药物的靶点对COVID-19的治疗具有积极意义。本研究应用生物信息学工具分析新型冠状病毒的木瓜样蛋白酶的结构和功能,首先利用BLAST和BioEdit获取SARS-CoV-2 PLpro蛋白酶(SC2-PLpro)及其同源蛋白的氨基酸序列,并利用BLAST和MEGA 6.0进行同源性分析。之后,利用ProParam和Proscale分别对SC2-PLpro蛋白酶的理化性质、亲水性和疏水性进行分析。然后,通过SOMPA、ScanProsite和InterPro分别预测SC2-PLpro蛋白酶的二级结构和功能区域,进一步利用SignalP 4.0和TMHMM对SC2-PLpro蛋白酶的信号肽和跨膜区进行分析。最后,通过SWISS-MODEL对SARS-CoV-2 PLpro蛋白酶进行三级结构同源建模。结果显示,对SARS-CoV-2 PLpro蛋白酶与已报道的PLpro蛋白酶进行多序列比对后,发现SARS-CoV-2 nsp3的746~1063段氨基酸与多种冠状病毒PLpro蛋白酶氨基酸序列高度相似。同时,同源性分析发现SARS-CoV-2与蝙蝠冠状病毒的PLpro蛋白酶具有同源性,其中与QHR63299、AVP78030相似性最高。对SC2-PLpro进行理化性质预测结果显示,其由318个氨基酸所组成,为稳定亲水性蛋白。二级结构预测结果显示SC2-PLpro主要含有α-螺旋、延伸链、β-转角、无规卷曲,四种结构贯穿整条氨基酸链。进一步进行功能分析,发现其具有完整的催化三联体、锌结合域、泛素样N末端结构域,故推测该蛋白具有去泛素化的功能。然后,信号肽假说和跨膜结构域分析结果表明,SC2-PLpro既不是分泌蛋白,也不属于跨膜蛋白。本研究提示,生物信息学分析SC2-PLpro为稳定性亲水蛋白,属于非跨膜蛋白,比较保守,具有去泛素化的功能,利用此功能可以进一步规避宿主的固有免疫反应。通过制备PLpro蛋白酶小分子抑制剂,可能有助于治疗新型冠状病毒肺炎。     

Evolution of a Protein-Folding Machine: Genomic and Evolutionary Analyses Reveal Three Lineages of the Archaeal hsp70(dnaK) Gene

The stress chaperone protein Hsp70 (DnaK) (abbreviated DnaK) and its co-chaperones Hsp40(DnaJ) (or DnaJ) and GrpE are universal in bacteria and eukaryotes but occur only in some archaea clustered in the order 5′-grpE-dnaK-dnaJ-3′ in a locus termed Locus I. Three structural varieties of Locus I, termed Types I, II, and III, were identified, respectively, in Methanosarcinales, in Thermoplasmatales and Methanothermobacter thermoautotrophicus, and in Halobacteriales. These Locus I types corresponded to three groups identified by phylogenetic trees of archaeal DnaK proteins including the same archaeal subdivisions. These archaeal DnaK groups were not significantly interrelated, clustering instead with DnaKs from three bacterial lineages, Methanosarcinales with Firmicutes, Thermoplasmatales and M. thermoautotrophicus with Thermotoga, and Halobacteriales with Actinobacteria, suggesting that the three archaeal types of Locus I were acquired by independent events of lateral gene transfer. These associations, however, lacked strong bootstrap support and were sensitive to dataset choice and tree-reconstruction method. Structural features of dnaK loci in bacteria revealed that Methanosarcinales and Firmicutes shared a similar structure, also common to most other bacterial groups. Structural differences were observed instead in Thermotoga compared to Thermoplasmatales and M. thermoautotrophicus, and in Actinobacteria compared to Halobacteriales. It was also found that the association between the DnaK sequences from Halobacteriales and Actinobacteria likely reflects common biases in their amino acid compositions. Although the loci structural features and the DnaK trees suggested the possibility of lateral gene transfer between Firmicutes and Methanosarcinales, the similarity between the archaeal and the ancestral bacterial loci favors the more parsimonious hypothesis that all archaeal sequences originated from a unique prokaryotic ancestor. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Stephen Freeland]     

Phragmoplastins,the Trentepohliales,and the Evolution of the Cytokinesis in Green Plants

Representatives of the monophyletic Trentepohliales are widely distributed in the tropics, subtropics, and temperate regions worldwide. They grow in soil, or are epilithic, epiphytic or endophytic. The family comprises approximately 70 species placed in at least four genera (Trentepohlia, Cephaleuros, Phycopeltis and Stomatochroon), with Trentepohlia sensu lato (including Printzina and Physolinum) accounting for half of the species in this family. PCR amplification and sequencing of the 18 SSU rDNA of 18 isolates of the Trentepohliaceae were used to assess the monophyly of the genus Cephaleuros and to determine the phylogenetic relationships among species of Trentepohlia sensu lato. Distance, Parsimony, and Maximum Likelihood analyses indicate that Trentepohlia sensu lato is basal and includes two species recently transferred to Phycopeltis (P. umbrina) and Printzina (P. lagenifera). In contrast, Cephaleuros is a derived monophyletic clade. Analysis of isolates of C. virescens, from the USA, Taiwan, and South Africa indicate that this taxon may consist of different species sharing a convergent morphology. The results of this study have implications for the taxonomy of the genera.     

Crystal Structure,SAXS and Kinetic Mechanism of Hyperthermophilic ADP-Dependent Glucokinase from Thermococcus litoralis Reveal a Conserved Mechanism for Catalysis

ADP-dependent glucokinases represent a unique family of kinases that belong to the ribokinase superfamily, being present mainly in hyperthermophilic archaea. For these enzymes there is no agreement about the magnitude of the structural transitions associated with ligand binding and whether they are meaningful to the function of the enzyme. We used the ADP-dependent glucokinase from Termococcus litoralis as a model to investigate the conformational changes observed in X-ray crystallographic structures upon substrate binding and to compare them with those determined in solution in order to understand their interplay with the glucokinase function. Initial velocity studies indicate that catalysis follows a sequential ordered mechanism that correlates with the structural transitions experienced by the enzyme in solution and in the crystal state. The combined data allowed us to resolve the open-closed conformational transition that accounts for the complete reaction cycle and to identify the corresponding clusters of aminoacids residues responsible for it. These results provide molecular bases for a general mechanism conserved across the ADP-dependent kinase family.     

Comparative Phylogenomics and Evolution of the Brucellae Reveal a Path to Virulence

Brucella species include important zoonotic pathogens that have a substantial impact on both agriculture and human health throughout the world. Brucellae are thought of as “stealth pathogens” that escape recognition by the host innate immune response, modulate the acquired immune response, and evade intracellular destruction. We analyzed the genome sequences of members of the family Brucellaceae to assess its evolutionary history from likely free-living soil-based progenitors into highly successful intracellular pathogens. Phylogenetic analysis split the genus into two groups: recently identified and early-dividing “atypical” strains and a highly conserved “classical” core clade containing the major pathogenic species. Lateral gene transfer events brought unique genomic regions into Brucella that differentiated them from Ochrobactrum and allowed the stepwise acquisition of virulence factors that include a type IV secretion system, a perosamine-based O antigen, and systems for sequestering metal ions that are absent in progenitors. Subsequent radiation within the core Brucella resulted in lineages that appear to have evolved within their preferred mammalian hosts, restricting their virulence to become stealth pathogens capable of causing long-term chronic infections.     

Structure and Function of the Hetero-oligomeric Cysteine Synthase Complex in Plants

Cysteine synthesis in bacteria and plants is catalyzed by serine acetyltransferase (SAT) and O-acetylserine (thiol)-lyase (OAS-TL), which form the hetero-oligomeric cysteine synthase complex (CSC). In plants, but not in bacteria, the CSC is assumed to control cellular sulfur homeostasis by reversible association of the subunits. Application of size exclusion chromatography, analytical ultracentrifugation, and isothermal titration calorimetry revealed a hexameric structure of mitochondrial SAT from Arabidopsis thaliana (AtSATm) and a 2:1 ratio of the OAS-TL dimer to the SAT hexamer in the CSC. Comparable results were obtained for the composition of the cytosolic SAT from A. thaliana (AtSATc) and the cytosolic SAT from Glycine max (Glyma16g03080, GmSATc) and their corresponding CSCs. The hexameric SAT structure is also supported by the calculated binding energies between SAT trimers. The interaction sites of dimers of AtSATm trimers are identified using peptide arrays. A negative Gibbs free energy (ΔG = −33 kcal mol⁻¹) explains the spontaneous formation of the AtCSCs, whereas the measured SAT:OAS-TL affinity (K_D = 30 nm) is 10 times weaker than that of bacterial CSCs. Free SAT from bacteria is >100-fold more sensitive to feedback inhibition by cysteine than AtSATm/c. The sensitivity of plant SATs to cysteine is further decreased by CSC formation, whereas the feedback inhibition of bacterial SAT by cysteine is not affected by CSC formation. The data demonstrate highly similar quaternary structures of the CSCs from bacteria and plants but emphasize differences with respect to the affinity of CSC formation (K_D) and the regulation of cysteine sensitivity of SAT within the CSC.     

海藻肽的化学结构特征和活性作用研究进展

海藻中的肽类化合物具有显著的生物活性和药理作用,对其氨基酸序列及活性作用的研究已经取得了一些重要进展。发现的海藻肽类化合物并确定其化学结构式的主要有二肽、环肽和脂肽,这些肽类化合物具有抗肿瘤、降血压、降血脂、抗凝血、促进神经细胞分化、抗氧化、抗菌和抗病毒等生物活性。预测海藻肽类化合物在疑难病症的治疗上将发挥重要作用。     

Structure and Function of the FeoB G-Domain from Methanococcus jannaschii

FeoB in bacteria and archaea is involved in the uptake of ferrous iron (Fe²⁺), an important cofactor in biological electron transfer and catalysis. Unlike any other known prokaryotic membrane protein, FeoB contains a GTP-binding domain at its N-terminus. We determined high-resolution X-ray structures of the FeoB G-domain from Methanococcus jannaschii with and without bound GDP or Mg²⁺-GppNHp. The G-domain forms the same dimer in all three structures, with the nucleotide-binding pockets at the dimer interface, as in the ATP-binding domain of ABC transporters. The G-domain follows the typical fold of nucleotide-binding proteins, with a β-strand inserted in switch I that becomes partially disordered upon GTP binding. Switch II does not contact the nucleotide directly and does not change its conformation in response to the bound nucleotide. Release of the nucleotide causes a rearrangement of loop L6, which we identified as the G5 region of FeoB. Together with the C-terminal helix, this loop may transmit the information about the nucleotide-bound state from the G-domain to the transmembrane region of FeoB.     

Identification of the Channelrhodopsin Genes in the Green and Cryptophytic Algae from the White and Black Seas

Biochemistry (Moscow) - Due to the unique capability of modulating cell membrane potential upon photoactivation, channelrhodopsins of green (Chlorophyta) and cryptophytic (Cryptophyta) algae are...     

Mechanism of Methane Transport from the Rhizosphere to the Atmosphere through Rice Plants

To clarify the mechanisms of methane transport from the rhizosphere into the atmosphere through rice plants (Oryza sativa L.), the methane emission rate was measured from a shoot whose roots had been kept in a culture solution with a high methane concentration or exposed to methane gas in the gas phase by using a cylindrical chamber. No clear correlation was observed between change in the transpiration rate and that in the methane emission rate. Methane was mostly released from the culm, which is an aggregation of leaf sheaths, but not from the leaf blade. Micropores which are different from stomata were newly found at the abaxial epidermis of the leaf sheath by scanning electron microscopy. The measured methane emission rate was much higher than the calculated methane emission rate that would result from transpiration and the methane concentration in the culture solution. Rice roots could absorb methane gas in the gas phase without water uptake. These results suggest that methane dissolved in the soil water surrounding the roots diffuses into the cell-wall water of the root cells, gasifies in the root cortex, and then is mostly released through the micropores in the leaf sheaths.     

Structure and Function of the Oxidoreductase DsbA1 from Neisseria meningitidis

Neisseria meningitidis encodes three DsbA oxidoreductases (NmDsbA1-NmDsbA3) that are vital for the oxidative folding of many membrane and secreted proteins, and these three enzymes are considered to exhibit different substrate specificities. This has led to the suggestion that each N. meningitidis DsbA (NmDsbA) may play a specialized role in different stages of pathogenesis; however, the molecular and structural bases of the different roles of NmDsbAs are unclear. With the aim of determining the molecular basis for substrate specificity and how this correlates to pathogenesis, we undertook a biochemical and structural characterization of the three NmDsbAs. We report the 2.0-Å-resolution crystal structure of the oxidized form of NmDsbA1, which adopted a canonical DsbA fold similar to that observed in the structures of NmDsbA3 and Escherichia coli DsbA (EcDsbA). Structural comparisons revealed variations around the active site and candidate peptide-binding region. Additionally, we demonstrate that all three NmDsbAs are strong oxidases with similar redox potentials; however, they differ from EcDsbA in their ability to be reoxidized by E. coli DsbB. Collectively, our studies suggest that the small structural differences between the NmDsbA enzymes and EcDsbA are functionally significant and are the likely determinants of substrate specificity.