Diversification of Two Lineages of Symbiotic Photobacterium

Understanding of processes driving bacterial speciation requires examination of closely related, recently diversified lineages. To gain an insight into diversification of bacteria, we conducted comparative genomic analysis of two lineages of bioluminescent symbionts, Photobacterium leiognathi and ‘P. mandapamensis’. The two lineages are evolutionary and ecologically closely related. Based on the methods used in bacterial taxonomy for classification of new species (DNA-DNA hybridization and ANI), genetic relatedness of the two lineages is at a cut-off point for species delineation. In this study, we obtained the whole genome sequence of a representative P. leiognathi strain lrivu.4.1, and compared it to the whole genome sequence of ‘P. mandapamensis’ svers.1.1. Results of the comparative genomic analysis suggest that P. leiognathi has a more plastic genome and acquired genes horizontally more frequently than ‘P. mandapamensis’. We predict that different rates of recombination and gene acquisition contributed to diversification of the two lineages. Analysis of lineage-specific sequences in 25 strains of P. leiognathi and ‘P. mandapamensis’ found no evidence that bioluminescent symbioses with specific host animals have played a role in diversification of the two lineages.     

MADS-box基因家族基因重复及其功能的多样性

基因的重复(duplication)及其功能的多样性(diversification)为生物体新的形态进化提供了原材料。MADS-box基因在植物(特别是被子植物)的进化过程中发生了大规模的基因重复事件而形成一个多基因家族。MADS-box基因家族的不同成员在植物生长发育过程中起着非常重要的作用,在调控开花时间、决定花分生组织和花器官特征以及调控根、叶、胚珠及果实的发育中起着广泛的作用。探讨MADS-box基因家族的进化历史有助于深入了解基因重复及随后其功能分化的过程和机制。本文综述了MADS-box基因家族基因重复及其功能分化式样的研究进展。     

Relation between the Light-Harvesting Chlorophyll a-Protein Complex LHCPa and Photosystem I in the Alga Chlamydobotrys stellata

The light-harvesting chlorophyll protein system of the alga Chlamydobotrys stellata consists of an as yet uncharacterized algal chlorophyll a-protein, called LHCPa, and a common photosystem II-related chlorophyll a/b-protein, called LHCPb (Brandt, Kaiser-Jarry, Wiessner 1982 Biochim Biophys Acta 679: 404-409). For further characterization, this LHCPa was isolated from the organism by polyacrylamide isoelectrofocusing and reelectrophoresis. It contains only chlorophyll a and has only one apoprotein (32,000 daltons). When separated from autotrophically grown cells, its absorption peak is at 674 nm and its isoelectric point at 5.3. Photoheterotrophic cultivation of the algae shifts the absorption maximum of LHCPa to 679 nm and its isoelectric point to 4.8. This LHCPa is a component of photosystem I particles. In relation to the total chlorophyll a content, the amount of LHCPa is low in autotrophic algae, but increases under photoheterotrophic growth conditions, where the organisms do not have the ability to assimilate CO₂ photosynthetically.     

Induction of Glycerol Synthesis and Release in Cultured Symbiodinium

Background

Symbiotic dinoflagellates transfer a substantial amount of their photosynthetic products to their animal hosts. This amount has been estimated to represent up to 90% of the photosynthetically fixed carbon and can satisfy in some instances the full respiratory requirements of the host. Although in several cnidarian-dinoflagellate symbioses glycerol is the primary photosynthetic product translocated to the host, the mechanism for its production and release has not been demonstrated conclusively.

Principal Findings

Using Symbiodinium cells in culture we were able to reproduce the synthesis and release of glycerol in vitro by employing an inductor for glycerol synthesis, osmotic up-shocks. Photosynthetic parameters and fluorescence analysis of photosystem II showed that the inductive conditions did not have a negative effect on photosynthetic performance, suggesting that the capacity for carbon fixation by the cells was not compromised. The demand for glycerol production required to attain osmotic balance increased the expression of ribulose 1,5-bisphosphate and of glycerol 3-phosphate dehydrogenase, possibly competing with the flux of fixed carbon necessary for protein synthesis. In longer exposures of cultured Symbiodinium cells to high osmolarity, the response was analogous to photoacclimation, reducing the excitation pressure over photosystem II, suggesting that Symbiodinium cells perceived the stress as an increase in light. The induced synthesis of glycerol resulted in a reduction of growth rates.

Conclusions

Our results favor a hypothetical mechanism of a signaling event involving a pressure sensor that may induce the flux of carbon (glycerol) from the symbiotic algae to the animal host, and strongly suggest that carbon limitation may be a key factor modulating the population of symbionts within the host.     

假根羽藻主要捕光叶绿素a/b-蛋白复合体的特性

应用阴离子交换和凝胶过滤层析技术,从假根羽藻(Bryopsis corticulans Setch.)类囊体膜中直接分离、纯化获得了主要叶绿素a/b-蛋白复合体(LHCⅡ).经蔗糖密度梯度超速离心获得了该色素蛋白复合体的单体和三聚体.反相液相色谱的色素分析结果显示,假根羽藻LHCⅡ的色素组成含有叶绿素a、叶绿素b、新黄质、紫黄质和管藻素等.其单体的电子跃迁能谱与三聚体的相似.园二色光谱分析显示,在LHCⅡ脱辅基蛋白质上分别存在着很强的叶绿素a偶极子之间和叶绿素b偶极子之间的分子内相互作用,然而这些偶极子之间的分子间的相互作用在三聚体中得到明显增强.在能量传递方面,LHCⅡ单体有着与三聚体相似的从叶绿素b到叶绿素a以及从管藻素到叶绿素a的高效传能能力.实验结果表明,假根羽藻中LHCⅡ单体具有像三聚体那样可以高效发挥吸能和传能生理功能的色素组成形式.因此,这些单体可能是假根羽藻类囊体膜上具有功能作用的LHCⅡ的结构形式.     

假根羽藻主要捕光叶绿素a/b-蛋白复合体的特性(英文)

应用阴离子交换和凝胶过滤层析技术,从假根羽藻(Bryopsis corticulans Setch. )类囊体膜中直接分离、纯化获得了主要叶绿素a/b-蛋白复合体(LHCⅡ)。经蔗糖密度梯度超速离心获得了该色素蛋白复合体的单体和三聚体。反相液相色谱的色素分析结果显示,假根羽藻LHCⅡ的色素组成含有叶绿素a、叶绿素b、新黄质、紫黄质和管藻素等。其单体的电子跃迁能谱与三聚体的相似。园二色光谱分析显示,在LHCⅡ脱辅基蛋白质上分别存在着很强的叶绿素a偶极子之间和叶绿素b偶极子之间的分子内相互作用,然而这些偶极子之间的分子间的相互作用在三聚体中得到明显增强。在能量传递方面,LHCⅡ单体有着与三聚体相似的从叶绿素b到叶绿素a以及从管藻素到叶绿素a的高效传能能力。实验结果表明,假根羽藻中LHCⅡ单体具有像三聚体那样可以高效发挥吸能和传能生理功能的色素组成形式。因此,这些单体可能是假根羽藻类囊体膜上具有功能作用的LHCⅡ的结构形式。     

Characterization of the PMT Gene Family in Cryptococcus neoformans

Background

Protein-O-mannosyltransferases (Pmt''s) catalyze the initial step of protein-O-glycosylation, the addition of mannose residues to serine or threonine residues of target proteins.

Methodology/Principal Findings

Based on protein similarities, this highly conserved protein family can be divided into three subfamilies: the Pmt1 sub-family, the Pmt2 sub-family and the Pmt4 sub-family. In contrast to Saccharomyces cerevisiae and Candida albicans, but similar to filamentous fungi, three putative PMT genes (PMT1, PMT2, and PMT4) were identified in the genome of the human fungal pathogen Cryptococcus neoformans. Similar to Schizosaccharomyces pombe and C. albicans, C. neoformans PMT2 is an essential gene. In contrast, the pmt1 and pmt4 single mutants are viable; however, the pmt1/pmt4 deletions are synthetically lethal. Mutation of PMT1 and PMT4 resulted in distinct defects in cell morphology and cell integrity. The pmt1 mutant was more susceptible to SDS medium than wild-type strains and the mutant cells were enlarged. The pmt4 mutant grew poorly on high salt medium and demonstrated abnormal septum formation and defects in cell separation. Interestingly, the pmt1 and pmt4 mutants demonstrated variety-specific differences in the levels of susceptibility to osmotic and cell wall stress. Delayed melanin production in the pmt4 mutant was the only alteration of classical virulence-associated phenotypes. However, the pmt1 and pmt4 mutants showed attenuated virulence in a murine inhalation model of cryptococcosis.

Conclusion/Significance

These findings suggest that C. neoformans protein-O-mannosyltransferases play a crucial role in maintaining cell morphology, and that reduced protein-O-glycosylation leads to alterations in stress resistance, cell wall composition, cell integrity, and survival within the host.     

Genome-Wide Identification of the Invertase Gene Family in Populus

Invertase plays a crucial role in carbohydrate partitioning and plant development as it catalyses the irreversible hydrolysis of sucrose into glucose and fructose. The invertase family in plants is composed of two sub-families: acid invertases, which are targeted to the cell wall and vacuole; and neutral/alkaline invertases, which function in the cytosol. In this study, 5 cell wall invertase genes (PtCWINV1-5), 3 vacuolar invertase genes (PtVINV1-3) and 16 neutral/alkaline invertase genes (PtNINV1-16) were identified in the Populus genome and found to be distributed on 14 chromosomes. A comprehensive analysis of poplar invertase genes was performed, including structures, chromosome location, phylogeny, evolutionary pattern and expression profiles. Phylogenetic analysis indicated that the two sub-families were both divided into two clades. Segmental duplication is contributed to neutral/alkaline sub-family expansion. Furthermore, the Populus invertase genes displayed differential expression in roots, stems, leaves, leaf buds and in response to salt/cold stress and pathogen infection. In addition, the analysis of enzyme activity and sugar content revealed that invertase genes play key roles in the sucrose metabolism of various tissues and organs in poplar. This work lays the foundation for future functional analysis of the invertase genes in Populus and other woody perennials.     

Sites of Intra- and Intermolecular Cross-linking of the N-terminal Extension of Troponin I in Human Cardiac Whole Troponin Complex

Our previous studies (Howarth, J. W., Meller, J., Solaro, R. J., Trewhella, J., and Rosevear, P. R. (2007) J. Mol. Biol. 373, 706–722) of the unique N-terminal region of human cardiac troponin I (hcTnI), predicted a possible intramolecular interaction near the basic inhibitory peptide. To explore this possibility, we generated single cysteine mutants (hcTnI-S5C and hcTnI-I19C), which were labeled with the hetero-bifunctional cross-linker benzophenone-4-maleimide. The labeled hcTnI was reconstituted to whole troponin and exposed to UV light to form cross-linked proteins. Reversed-phase high-performance liquid chromatography and SDS-PAGE indicated intra- and intermolecular cross-linking with hcTnC and hcTnT. Moreover, using tandem mass spectrometry and Edman sequencing, specific intramolecular sites of interaction were determined at position Met-154 (I19C mutant) and Met-155 (S5C mutant) of hcTnI and intermolecular interactions at positions Met-47 and Met-80 of hcTnC in all conditions. Even though specific intermolecular cross-linked sites did not differ, the relative abundance of cross-linking was altered. We also measured the Ca²⁺-dependent ATPase rate of reconstituted thin filament-myosin-S1 preparation regulated by either cross-linked or non-labeled troponin. Ca²⁺ regulation of the ATPase rate was lost when the Cys-5 hcTnI mutant was cross-linked in the absence of Ca²⁺, but only partially inhibited with Cys-19 cross-linking in either the presence or absence of Ca²⁺. This result indicates different functional effects of cross-linking to Met-154 and Met-155, which are located on different sides of the hcTnI switch peptide. Our data provide novel evidence identifying interactions of the hcTnI-N terminus with specific intra- and intermolecular sites.The human cardiac variant of troponin I (hcTnI)² has structural and functional specializations that are related to its critical role in control of cardiac dynamics. These specializations include variations in amino acids that are significant factors in the response of the heart to: adrenergic stimulation (1), sarcomere length (2, 3), and pH (4, 5). An especially significant region of specialization is a unique N-terminal extension of 30–32 amino acids, which contains serial serines at positions 23/24 that are substrates for kinases that control cardiac dynamics (6–8). Despite its significance in control of cardiac function, molecular mechanisms of how the N-terminal human cardiac troponin I (N-hcTnI) region controls sarcomeric and cardiac function remain poorly understood. There is evidence that upon phosphorylation the interaction between the N-hcTnI and the N-lobe of N-hcTnC is weakened (9, 10). The structure of the N-hcTnI was missing in the crystal structure of cardiac troponin (11). However, we recently reported (12) the structure of the N-terminal peptide using NMR. Docking of this structure into the core troponin structure indicated the potential for a previously unappreciated intramolecular interactions of the N terminus with the regions at or near the highly basic inhibitory peptide region of cardiac troponin (12, 13). This interaction appeared plausible not only on the basis of the structure of hcTnI, but also on the basis of the preponderance of basic amino acids in the inhibitory peptide and the presence of acidic residues in the N terminus.In experiments reported here, we tested the hypothesis that the unique N-terminal region of hcTnI engages in both intra- and intermolecular interactions. We introduced Cys residues into the N-hcTnI at positions 5 and 19 and labeled the Cys residue with the hetero-bifunctional cross-linker, BP-MAL, which upon UV irradiation cross-links to residues within ∼10 Å of the modified Cys (14). We analyzed the cross-linked peptides by Edman sequencing and mass spectrometry to determine specific sites of interaction. The intramolecular sites of interaction were Met-154 and Met-155 in the hcTnI switch peptide for labeled positions 19 and 5, respectively. The intermolecular cross-linking sites on N-hcTnC were 47 and 80 for hcTnI labeled at either position 5 or 19. Measurement of Ca²⁺-dependent ATPase rate in reconstituted preparations indicated that allosteric effects of the different specific intramolecular cross-links (position Met-154 versus Met-155) to different hydrophobic positions on the switch peptide may affect hcTnC interaction with the switch peptide.     

Implications of a Developmental-Stage-Dependent Thylakoid-Bound Protease in the Stabilization of the Light-Harvesting Pigment-Protein Complex Serving Photosystem II during Thylakoid Biogenesis in Red Kidney Bean

Intact etioplasts of bean (Phaseolus vulgaris) plants exhibit proteolytic activity against the exogenously added apoprotein of the light-harvesting pigment-protein complex serving photosystem II (LHCII) that increases as etiolation is prolonged. The activity increases in the membrane fraction but not in the stroma, where it remains low and constant and is mainly directed against LHCII and protochlorophyllide oxidoreductase. The thylakoid proteolytic activity, which is low in etioplasts of 6-d-old etiolated plants, increases in plants pretreated with a pulse of light or exposed to intermittent-light (ImL) cycles, but decreases during prolonged exposure to continuous light, coincident with chlorophyll (Chl) accumulation. To distinguish between the control of Chl and/or development on proteolytic activity, we used plants exposed to ImL cycles of varying dark-phase durations. In ImL plants exposed to an equal number of ImL cycles with short or long dark intervals (i.e. equal Chl accumulation but different developmental stage) proteolytic activity increased with the duration of the dark phase. In plants exposed to ImL for equal durations to such light-dark cycles (i.e. different Chl accumulation but same developmental stage) the proteolytic activity was similar. These results suggest that the protease, which is free to act under limited Chl accumulation, is dependent on the developmental stage of the chloroplast, and give a clue as to why plants in ImL with short dark intervals contain LHCII, whereas those with long dark intervals possess only photosystem-unit cores and lack LHCII.     

Characterization of the Pichia pastoris Protein-O-mannosyltransferase Gene Family

The methylotrophic yeast, Pichia pastoris , is an important organism used for the production of therapeutic proteins. However, the presence of fungal-like glycans, either N-linked or O-linked, can elicit an immune response or enable the expressed protein to bind to mannose receptors, thus reducing their efficacy. Previously we have reported the elimination of β-linked glycans in this organism. In the current report we have focused on reducing the O-linked mannose content of proteins produced in P . pastoris , thereby reducing the potential to bind to mannose receptors. The initial step in the synthesis of O-linked glycans in P . pastoris is the transfer of mannose from dolichol-phosphomannose to a target protein in the yeast secretory pathway by members of the protein-O-mannosyltransferase (PMT) family. In this report we identify and characterize the members of the P . pastoris PMT family. Like Candida albicans, P . pastoris has five PMT genes. Based on sequence homology, these PMTs can be grouped into three sub-families, with both PMT1 and PMT2 sub-families possessing two members each (PMT1 and PMT5, and PMT2 and PMT6, respectively). The remaining sub-family, PMT4, has only one member (PMT4). Through gene knockouts we show that PMT1 and PMT2 each play a significant role in O-glycosylation. Both, by gene knockouts and the use of Pmt inhibitors we were able to significantly reduce not only the degree of O-mannosylation, but also the chain-length of these glycans. Taken together, this reduction of O-glycosylation represents an important step forward in developing the P . pastoris platform as a suitable system for the production of therapeutic glycoproteins.     

The Existence of Chlorophyll c in the Chl b-Containing,Light-Harvesting Complex of the Green Alga Mantoniella squamata (Prasinophyceae)

The prasinophycean alga Mantoniella contains, in addition to Chl a and b, at least a third green pigment which is functionally active in the light-harvesting antenna. This third Chl was isolated in order to elucidate its chemical structure. The absorption and fluorescence spectra were measured not only from the purified pigment but also from its pheophytin and its methylpheophorbide. The spectra were compared with those of authentic Chl c-1 and c-2, which were isolated from the diatom Nitzschia sp. and with Mg-DVPP (purified from Rhodobacter). The results show that the pigment from Mantoniella compares best with Chl c-1. In order to clarify the spectral data, Chl c-1 and c-2, Mg-DVPP, and the pigment from Mantoniella were subjected to a chromatographic system that is able to separate these porphyrins. The chromatographic analysis clearly shows that the pigment from Mantoniella co-migrates with Chl c-1 and not with the bacterial pigment. Mantoniella is the first organism which has been demonstrated to contain Chl a, b, and authentic c.     

Development of a Heat-Shock Inducible Gene Expression System in the Red Alga Cyanidioschyzon merolae

The cell of the unicellular red alga Cyanidioschyzon merolae contains a single chloroplast and mitochondrion, the division of which is tightly synchronized by a light/dark cycle. The genome content is extremely simple, with a low level of genetic redundancy, in photosynthetic eukaryotes. In addition, transient transformation and stable transformation by homologous recombination have been reported. However, for molecular genetic analyses of phenomena that are essential for cellular growth and survival, inducible gene expression/suppression systems are needed. Here, we report the development of a heat-shock inducible gene expression system in C. merolae. CMJ101C, encoding a small heat shock protein, is transcribed only when cells are exposed to an elevated temperature. Using a superfolder GFP as a reporter protein, the 200-bp upstream region of CMJ101C orf was determined to be the optimal promoter for heat-shock induction. The optimal temperature to induce expression is 50°C, at which C. merolae cells are able to proliferate. At least a 30-min heat shock is required for the expression of a protein of interest and a 60-min heat shock yields the maximum level of protein expression. After the heat shock, the mRNA level decreases rapidly. As an example of the system, the expression of a dominant negative form of chloroplast division DRP5B protein, which has a mutation in the GTPase domain, was induced. Expression of the dominant negative DRP5B resulted in the appearance of aberrant-shaped cells in which two daughter chloroplasts and the cells are still connected by a small DRP5B positive tube-like structure. This result suggests that the dominant negative DRP5B inhibited the final scission of the chloroplast division site, but not the earlier stages of division site constriction. It is also suggested that cell cycle progression is not arrested by the impairment of chloroplast division at the final stage.     

Diet and Diversification in the Evolution of Coral Reef Fishes

The disparity in species richness among evolutionary lineages is one of the oldest and most intriguing issues in evolutionary biology. Although geographical factors have been traditionally thought to promote speciation, recent studies have underscored the importance of ecological interactions as one of the main drivers of diversification. Here, we test if differences in species richness of closely related lineages match predictions based on the concept of density-dependent diversification. As radiation progresses, ecological niche-space would become increasingly saturated, resulting in fewer opportunities for speciation. To assess this hypothesis, we tested whether reef fish niche shifts toward usage of low-quality food resources (i.e. relatively low energy/protein per unit mass), such as algae, detritus, sponges and corals are accompanied by rapid net diversification. Using available molecular information, we reconstructed phylogenies of four major reef fish clades (Acanthuroidei, Chaetodontidae, Labridae and Pomacentridae) to estimate the timing of radiations of their subclades. We found that the evolution of species-rich clades was associated with a switch to low quality food in three of the four clades analyzed, which is consistent with a density-dependent model of diversification. We suggest that ecological opportunity may play an important role in understanding the diversification of reef-fish lineages.     

Functional Rearrangement of the Light-Harvesting Antenna upon State Transitions in a Green Alga

State transitions in the green alga Chlamydomonas reinhardtii serve to balance excitation energy transfer to photosystem I (PSI) and to photosystem II (PSII) and possibly play a role as a photoprotective mechanism. Thus, light-harvesting complex II (LHCII) can switch between the photosystems consequently transferring more excitation energy to PSII (state 1) or to PSI (state 2) or can end up in LHCII-only domains. In this study, low-temperature (77 K) steady-state and time-resolved fluorescence measured on intact cells of Chlamydomonas reinhardtii shows that independently of the state excitation energy transfer from LHCII to PSI or to PSII occurs on two main timescales of <15 ps and ∼100 ps. Moreover, in state 1 almost all LHCIIs are functionally connected to PSII, whereas the transition from state 1 to a state 2 chemically locked by 0.1 M sodium fluoride leads to an almost complete functional release of LHCIIs from PSII. About 2/3 of the released LHCIIs transfer energy to PSI and ∼1/3 of the released LHCIIs form a component designated X-685 peaking at 685 nm that decays with time constants of 0.28 and 5.8 ns and does not transfer energy to PSI or to PSII. A less complete state 2 was obtained in cells incubated under anaerobic conditions without chemical locking. In this state about half of all LHCIIs remained functionally connected to PSII, whereas the remaining half became functionally connected to PSI or formed X-685 in similar amounts as with chemical locking. We demonstrate that X-685 originates from LHCII domains not connected to a photosystem and that its presence introduces a change in the interpretation of 77 K steady-state fluorescence emission measured upon state transitions in Chalamydomonas reinhardtii.