Evidence for positive selection in phycoerythrin genes of red algae and cyanobacteria Prochlorococcus and Synechococcus

Because of the shortage of phycoerythrin (PE) gene sequences from rhodophytes, peBA encoding beta- and alpha-subunits of PE from three species of red algae (Ceramium boydenn, Halymenia sinensis, and Plocamium telfariae) were cloned and sequenced. Different selection forces have affected the evolution of PE lineages. 8.9 % of the codons were subject to positive selection within the PE lineages (excluding high-irradiance adapted Prochlorococcus). More than 40 % of the sites may be under positive selection, and nearly 20 % sites are weakly constraint sites in high-irradiance adapted Prochlorococcus. Sites most likely undergoing positive selection were found in the chromophore binding domains, suggesting that these sites have played important roles in environmental adaptation during PE diversification. Moreover, the heterogeneous distribution of positively selected sites along the PE gene was revealed from the comparison of low-irradiance adapted Prochlorococcus and marine Synechococcus, which firmly suggests that evolutionary patterns of PEs in these two lineages are significantly different.

Comparative molecular population genetics of phycoerythrin locus in Prochlorococcus

As the only remainder type of phycobiliproteins in Prochlorococcus, the actual role of phycoerythrin still remains unknown. Previous studies revealed that two different forms of phycoerythrin gene were found in two ecotypes of Prochlorococcus that are specifically adapted to either high light (HL) or low light (LL) conditions. Here we analyze patterns of phycoerythrin nucleotide variation in the HL- and LL-Prochlorococcus populations. Our analyses reveal a significantly greater number of non-synonymous fixed substitutions in peB and peA than expected based on interspecific comparisons. This pattern of excess non-synonymous fixed substitutions is not seen in other five phycoerythrin-related genes (peZ/V/Y/T/S). Several neutrality statistical tests indicate an excess of rare frequency polymorphisms in the LL-Prochlorococcus data, but an excess of intermediate frequency polymorphisms in the HL-Prochlorococcus data. Distributions of the positively selected sites identified using the likelihood ratio test, when mapped onto the phycoerythrin tertiary structure, reveal that HL- and LL-phycoerythrin should be under different selective patterns. These findings may provide insights into the likely role of selection at the phycoerythrin locus and motivate further research to unveil the function of phycoerythrin in Prochlorococcus.

Comparative Analysis of Fatty Acid Desaturases in Cyanobacterial Genomes

Fatty acid desaturases are enzymes that introduce double bonds into the hydrocarbon chains of fatty acids. The fatty acid desaturases from 37 cyanobacterial genomes were identified and classified based upon their conserved histidine-rich motifs and phylogenetic analysis, which help to determine the amounts and distributions of desaturases in cyanobacterial species. The filamentous or N-2-fixing cyanobacteria usually possess more types of fatty acid desaturases than that of unicellular species. The pathway of acyl-lipid desaturation for unicellular marine cyanobacteria Synechococcus and Prochlorococcus differs from that of other cyanobacteria, indicating different phylogenetic histories of the two genera from other cyanobacteria isolated from freshwater, soil, or symbiont. Strain Gloeobacter violaceus PCC 7421 was isolated from calcareous rock and lacks thylakoid membranes. The types and amounts of desaturases of this strain are distinct to those of other cyanobacteria, reflecting the earliest divergence of it from the cyanobacterial line. Three thermophilic unicellular strains, Thermosynechococcus elongatus BP-1 and two Synechococcus Yellowstone species, lack highly unsaturated fatty acids in lipids and contain only one Delta 9 desaturase in contrast with mesophilic strains, which is probably due to their thermic habitats. Thus, the amounts and types of fatty acid desaturases are various among different cyanobacterial species, which may result from the adaption to environments in evolution. Copyright (c) 2008 Xiaoyuan Chi et al.

Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

Background: Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. Results: 286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains. Conclusion: The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.

Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

Background: Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. Results: 286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains. Conclusion: The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.

中国典型海域超微型生物生态学初步研究

通过流式细胞技术(FCM)调查了我国东海、南海和胶州湾的几类超微型浮游生物，包括聚球藻(Synechococcus)，原绿球藻(Prochlorococcus)，超微型真核生物和异养细菌的空间分布、季节变化及与环境因子之间的关系。开展了一系列现场实验对几种常量和微量营养元素对4类超微型浮游生物生长的影响进行了初步的研究。另外，对细胞周期法估计原绿球藻的生长率，以及用流式细胞仪分析病毒粒子的数量分布做了尝试性的工作。主要结果如下： 1 在东海黑潮区，超微型浮游植物约占叶绿素生物量的60％多，在其它海区，约占10-40％。原绿球藻的季节变化较大，冬季主要分布在黑潮流域，夏季可达50米等深线附近。在黑潮区，原绿球藻与聚球藻细胞密度的比值在10左右，在其它海区，比值为1-2。超微型浮游生物群落结构从沿岸到外海变化较复杂。在南海，平均70％多的叶绿素生物量由超微型浮游植物提供，而原绿球藻则为超微型自养浮游生物碳生物量的主要贡献者，平均约占30％。整个南海在海水性质上接近贫营养大洋海区，原绿球藻和聚球藻的细胞密度比为15～160，海盆区和岛礁区超微型浮游生物群落结构有所差别。 超微型浮游生物的分布和群落结构在两个海区均受海流、水团及水柱理化性质的影响。总的看来，海流、水团的性质越接近大洋，超微型浮游生物在生态系统中的地位相对越重要，而原绿球藻在生物量和生产力上的相对贡献也越大。原绿球藻在东海的分布除受水流、水团的作用外，在冬季还受温度的限制。冬季原绿球藻大体限于黑潮流域，而夏季则可分布到50米等深线附近。从大尺度范围看，从近岸到外海，或从中营养海区到贫营养海区过渡的过程中，原绿球藻和异养细菌的丰度变化呈相反趋势，它们与聚球藻之间的变化趋势因海区的不同而存有差异，这可能是由于多品系聚球藻同时存在的原因。这些相关性在水质条件变化幅度剧烈的东海表现得显著，而在海水水质条件差别不大的南海则不明显。在垂直分布上，超微型浮游植物的分布与水柱的分层、营养状况都有关系。在上混合层较浅，硝酸盐在检测限以上的东海大部分海区，超微型浮游植物的最大层与硝酸盐跃层深度有关，而在上混合层较深，混合层中硝酸盐的浓度低于检测限的南海海盆区，原绿球藻的高值分布似乎与氨氮的浓度有关。小尺度范围内超微型浮游生物的数量和群落结构的变化不仅与温度，营养盐浓度有关，还与水柱的物理结构(如混合层发育的情况)有关。 2 南海营养盐添加实验表明，原绿球藻似乎更受磷限制，而聚球藻和超微型真核生物对铵氮的添加反应更明显。在生理上，原绿球藻与聚球藻和超微型真核浮游植物有明显差别，后两者对营养盐添加的反应接近。原绿球藻对钴添加的反应大于铁添加的反应，而后两者则对铁添加的反应较强。在某些营养生理特性上，原绿球藻似乎更接近异养细菌。 75米层海水铁添加实验表明，不同浓度的铁均促进nano一级的浮游植物的生长；对于超微型浮游植物来说，纳摩尔级铁的添加有利于超微型真核生物的生长，而更高浓度的铁添加则对聚球藻和原绿球藻的生长有利。 虽然钴的加入有利于原绿球藻的生长，但是维生素B_(12)的加入对其生长无明显的影响，说明钴在原绿球藻的生理代谢过程中可能有合成维生素B_(12)以外的作用。钴的添加对聚球藻的生长无明显影响，但不同浓度的维生素B_(12)的添加均能促进聚球藻的生长，说明火洋中的聚球藻品系可能不能自己合成该种维生素。无论是钴还是维生素B_(12)对超微型真核生物的生长均无显著的影响。 钼与铁均参与硝酸盐的还原和固氮作用，但钼的添加只对聚球藻有明显的促进作用，对其它几类超微型浮游生物的影响不明显。 3 现场培养实验表明，原绿球藻在生理上能耐受的温度下限比其自然分布的温度下限更低，说明冬季限制原绿球藻向近岸分布的是多种环境因子共同作用的结果。实验表明，种间相互作用，微量金属元素，以及水体的物理化学条件等都是制约原绿球藻近岸分布的因素。 4 细胞周期法估计南海75米层原绿球藻的生长率为0.54／天。 5 流式细胞仪在东海东部检测一类病毒粒子的数量在10~5／毫升的数量级。尽管这类病毒粒子在垂直分布上与自养细胞的分布有关，但是在水平分布上却与异养细菌数量的变化相关性最显著。 6 胶州湾超微型浮游植物主要出聚球藻和超微型真核生物组成。聚球藻的细胞浓度在夏季最高，冬季细胞浓度最低，平均为1.4 8*10~3细胞／毫升，并与温度变化的关系最明显。超微型真核生物细胞浓度的季节变化不如聚球藻规律。从全年变化的角度来看，超微型浮游植物在胶州湾生态系统中占有重要的地位，而超微型真核生物是超微型浮游植物生物量的主要提供者。

Close coupling between phytoplankton growth and microzooplankton grazing in the western South China Sea

We conducted 28 dilution experiments during August-September 2007 to investigate the coupling of growth and microzooplankton grazing rates among ultraphytoplankton populations and the phytoplankton community and their responses to habitat variability (open-ocean oligotrophy, eddy-induced upwelling, and the Mekong River plume) in the western South China Sea. At the community level, standing stocks, growth, and grazing rates were strongly and positively correlated, and were related to the higher abundance of larger phytoplankton cells (diatoms) at stations with elevated chlorophyll concentration. Phytoplankton growth rates were highest (> 2 d(-1)) within an eastward offshore jet at 13 degrees N and at a station influenced by the river plume. Among ultraphytoplankton populations, Prochlorococcus dominated the more oceanic and oligotrophic stations characterized by generally lower biomass and phytoplankton community growth, whereas Synechococcus became more important in mesotrophic areas (eddies, offshore jet, and river plume). The shift to Synechococcus dominance reflected, in part, its higher growth rates (0.87 +/- 0.45 d(-1)) compared to Prochlorococcus (0.65 +/- 0.29 d(-1)) or picophytoeukaryotes (0.54 +/- 0.50 d(-1)). However, close coupling of microbial mortality rates via common predators is seen to play a major role in driving the dominance transition as a replacement of Prochlorococcus, rather than an overprinting of its steady-state standing stock.