The Evolution Pathway of Ammonia-Oxidizing Archaea Shaped by Major Geological Events

Primordial nitrification processes have been studied extensively using geochemical approaches, but the biological origination of nitrification remains unclear. Ammonia-oxidizing archaea (AOA) are widely distributed nitrifiers and implement the rate-limiting step in nitrification. They are hypothesized to have been important players in the global nitrogen cycle in Earth’s early history. We performed systematic phylogenomic and marker gene analyses to elucidate the diversification timeline of AOA evolution. Our results suggested that the AOA ancestor experienced terrestrial geothermal environments at ∼1,165 Ma (1,928–880 Ma), and gradually evolved into mesophilic soil at ∼652 Ma (767–554 Ma) before diversifying into marine settings at ∼509 Ma (629–412 Ma) and later into shallow and deep oceans, respectively. Corroborated by geochemical evidence and modeling, the timing of key diversification nodes can be linked to the global magmatism and glaciation associated with the assembly and breakup of the supercontinent Rodinia, and the later oxygenation of the deep ocean. Results of this integrated study shed light on the geological forces that may have shaped the evolutionary pathways of the AOA, which played an important role in the ancient global nitrogen cycle.     

Crystal structure of an archaeal actin homolog

Prokaryotic homologs of the eukaryotic structural protein actin, such as MreB and ParM, have been implicated in determination of bacterial cell shape, and in the segregation of genomic and plasmid DNA. In contrast to these bacterial actin homologs, little is known about the archaeal counterparts. As a first step, we expressed a predicted actin homolog of the thermophilic archaeon Thermoplasma acidophilum, Ta0583, and determined its crystal structure at 2.1A resolution. Ta0583 is expressed as a soluble protein in T.acidophilum and is an active ATPase at physiological temperature. In vitro, Ta0583 forms sheets with spacings resembling the crystal lattice, indicating an inherent propensity to form filamentous structures. The fold of Ta0583 contains the core structure of actin and clearly belongs to the actin/Hsp70 superfamily of ATPases. Ta0583 is approximately equidistant from actin and MreB on the structural level, and combines features from both eubacterial actin homologs, MreB and ParM. The structure of Ta0583 co-crystallized with ADP indicates that the nucleotide binds at the interface between the subdomains of Ta0583 in a manner similar to that of actin. However, the conformation of the nucleotide observed in complex with Ta0583 clearly differs from that in complex with actin, but closely resembles the conformation of ParM-bound nucleotide. On the basis of sequence and structural homology, we suggest that Ta0583 derives from a ParM-like actin homolog that was once encoded by a plasmid and was transferred into a common ancestor of Thermoplasma and Ferroplasma. Intriguingly, both genera are characterized by the lack of a cell wall, and therefore Ta0583 could have a function in cellular organization.     

镉对小鼠精母细胞凋亡及附睾内精子质量的影响

采用人工水质染毒的方法,利用透射电镜技术及流式细胞术（FCM）,探讨重金属镉对小鼠精巢内生殖细胞凋亡及附睾内成熟精子质量的影响.结果表明：各试验组小鼠生殖细胞处于凋亡时期的数量显著高于对照组,凋亡时期的生殖细胞超微结构呈现出线粒体空泡、核膜内陷、染色质周缘化及核固缩等形态特征,表明镉容易引起小鼠生殖细胞凋亡;各试验组精子早期凋亡的比例显著高于对照组,而活性精子的比例显著低于对照组（P<0.05）,其中高剂量组（0.10 mmol·L^-1）精子成活率（75.1%）显著低于对照组和其他试验组,而早期凋亡率（22.6%）则显著高于对照组;高剂量组睾丸生殖细胞DNA断裂率（18.2%）及附睾精子断裂率（26.5%）均显著高于对照组（3.3%、5.6 %）（P<0.05）.各试验组小鼠睾丸内DNA断裂的生殖细胞数量低于附睾内DNA断裂的精子数量.随着添加剂量的增加,小鼠睾丸内生殖细胞及附睾内精子凋亡率逐渐升高.表明小鼠生殖细胞凋亡及DNA损伤数量与镉剂量具有一定相关性.     

云南黑井古盐矿可培养极端嗜盐古菌初步研究*

从云南禄丰县黑井古镇古盐矿采集30多个盐土样品,用6种极端嗜盐古菌的培养基进行分离,共挑选出425株嗜盐菌。经过盐浓度耐受等实验筛选并去除可能重复菌株后共有79株极端嗜盐菌,选出15株进行了16S rRNA基因序列测定,结果显示,其中11株为极端嗜盐古菌。对这11株菌进行初步系统发育分析发现,它们广泛分布在极端嗜盐古菌科至少4个不同属中,其中16S rRNA基因和已有效发表种间的序列相似性在97％以上的有6株,分布在Halorubrum,Natronococcus,Natrialba,Halalkalicoccus4个属中;序列相似性低于97％的有5株：菌株YIM-ARC 0032,YIM-ARC 0036,YIM-ARC 0037,YIM-ARC 0050,它们的分类地位有待进一步确定。实验初步显示出了云南黑井盐矿极端嗜盐古菌的多样性和丰富度,值得深入研究。     

An Oscillating MinD Protein Determines the Cellular Positioning of the Motility Machinery in Archaea

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Tetramethylammonium:coenzyme M methyltransferase system from Methanococcoides sp.

A methanogen (strain NaT1) that belongs to the family of Methanosarcinaceae and that can grow on tetramethylammonium as the sole energy source has recently been isolated. We report here that cell extracts of the archaeon catalyze the formation of methyl-coenzyme M from coenzyme M and tetramethylammonium. The activity was dependent on the presence of Ti(III) citrate and ATP, and was rapidly lost under oxic conditions. Anoxic chromatography on DEAE-Sepharose revealed that two fractions, fractions 3 and 4, were required for activity. A 50-kDa protein that together with fraction 3 catalyzed methyl-coenzyme M formation from tetramethylammonium and coenzyme M was purified from fraction 4. From fraction 3, a 22-kDa corrinoid protein and a 40-kDa protein exhibiting methylcobalamin:coenzyme M methyltransferase (MT2) activity were purified. The N-terminal amino acid sequences of these purified proteins were determined. The 40-kDa protein showed sequence similarity to MT2 isoenzymes from Methanosarcina barkeri. Cell extract of strain NaT1 grown on trimethylamine rather than on tetramethylammonium did not exhibit tetramethylammonium:coenzyme M methyltransferase activity. The strain was identified as belonging to the genus of Methanococcoides, its closest relative being Methanococcoides methylutens. Received: 7 April 1998 / Accepted: 26 June 1998     

Structure and Function of the A1A0-ATPases from Methanogenic Archaea

Recent molecular studies revealed nine to ten gene products involved infunction/assembly of the methanoarchaeal ATPase and unravel a closerelationship of the A₁A₀-ATPase and theV₁V₀-ATPase with respect to subunit composition and thestructure of individual subunits. Most interestingly, there is anastonishing variability in the size of the proteolipids in methanoar chaealA₁A₀-ATPases with six, four, or two transmembranehelices and a variable number of conserved protonizable groups per monomer.Despite the structural similarities the A₁A₀-ATPasediffers fundamentally from the V₁V₀-ATPase by itsability to synthesize ATP, a feature shared withF₁F₀-ATPases. The discovery of duplicated andtriplicated versions of the proteolipid in A₁A₀-ATPsynthases questions older views of the structural requirements for ATPsynthases versus ATP hydrolases and sheds new light on the evolutionof these secondary energy converters.     

Identification of iron-regulated outer membrane proteins in uropathogenic Proteus mirabilis and its relationship with heme uptake

The effect of iron deprivation on the expression of outer membrane proteins and the ability to use heme as an iron source by uropathogenic Proteus mirabilis , Pr 6515, was studied. Examination of iron-restricted bacteria showed three outer membrane proteins ranging from 66 to 75 kDa to be affected by iron restriction, as well as a newly expressed 64-kDa protein. These proteins were induced within 15 minutes of iron-deprivation. The strain grew in the presence of ferric citrate, hemin and hemoglobin as iron sources, but could not use transferrin, lactoferrin or siderophores from exogenous sources. The 64- and 66-kDa proteins showed hemin-binding activity by affinity chromatography, and both reacted in Western blots with sera from mice transurethrally infected with the same strain. We suggest that P. mirabilis expresses iron-regulated outer membrane proteins that could be involved in heme uptake and may have a role in pathogenesis.