Target selection and deselection at the Berkeley Structural Genomics Center

At the Berkeley Structural Genomics Center (BSGC), our goal is to obtain a near-complete structural complement of proteins in the minimal organisms Mycoplasma genitalium and M. pneumoniae, two closely related pathogens. Current targets for structure determination have been selected in six major stages, starting with those predicted to be most tractable to high throughput study and likely to yield new structural information. We report on the process used to select these proteins, as well as our target deselection procedure. Target deselection reduces experimental effort by eliminating targets similar to those recently solved by the structural biology community or other centers. We measure the impact of the 69 structures solved at the BSGC as of July 2004 on structure prediction coverage of the M. pneumoniae and M. genitalium proteomes. The number of Mycoplasma proteins for which the fold could first be reliably assigned based on structures solved at the BSGC (24 M. pneumoniae and 21 M. genitalium) is approximately 25% of the total resulting from work at all structural genomics centers and the worldwide structural biology community (94 M. pneumoniae and 86 M. genitalium) during the same period. As the number of structures contributed by the BSGC during that period is less than 1% of the total worldwide output, the benefits of a focused target selection strategy are apparent. If the structures of all current targets were solved, the percentage of M. pneumoniae proteins for which folds could be reliably assigned would increase from approximately 57% (391 of 687) at present to around 80% (550 of 687), and the percentage of the proteome that could be accurately modeled would increase from around 37% (254 of 687) to about 64% (438 of 687). In M. genitalium, the percentage of the proteome that could be structurally annotated based on structures of our remaining targets would rise from 72% (348 of 486) to around 76% (371 of 486), with the percentage of accurately modeled proteins would rise from 50% (243 of 486) to 58% (283 of 486). Sequences and data on experimental progress on our targets are available in the public databases TargetDB and PEPCdb.     

猪肺炎支原体及其他支原体黏附因子的研究进展

猪肺炎支原体能够引起猪支原体肺炎,其黏附因子在致病过程中起重要作用。本文综合国内外猪肺炎支原体黏附因子的研究进展,并与其他支原体的黏附因子进行了比较讨论,从而为猪肺炎支原体致病机理的进一步研究及该病的防制提供新思路。     

Tetrazolium reduction methods for assessment of substrate oxidation and strain differentiation among mycoplasmas, with particular reference to Mycoplasma bovigenitalium and some members of the Mycoplasma mycoides cluster

Aims:  To apply a rapid nitroblue tetrazolium (NBT) reduction assay of substrate metabolism by mycoplasmas that would help to differentiate Mycoplasmas .
Methods and Results:  Growth, substrate preferences and tetrazolium reduction were assessed for 18 strains of Mycoplasma bovigenitalium and Mycoplasma ovine serogroup 11. NBT reduction was detectable in 1 h with 10⁸ CFU ml⁻¹. Use of α-ketobutyrate, lactate and pyruvate to support growth and NBT reduction were correlated: pyruvate was preferred and lactate was used by only four of the 18 strains. Selected members of the Mycoplasma mycoides cluster were also assessed and monotetrazoles tested as alternatives to NBT. The NBT method was applied to a further 19 species.
Conclusions:  This simple and reproducible method requires only small amounts of cells, enabling routine assessment of substrate use within 1 h, and the rapid assignment of numerous mycoplasmas to one of six physiological groups. The four physiological groups of M. bovigenitalium and Mycoplasma serogroup 11 strains were indistinguishable from each other, which supports the view that these belong to the same species.
Significance and Impact of the Study:  Strain-specific substrate-utilization patterns by mycoplasmas can be obtained rapidly and reliably. The method has potential as a large-scale semi-automated procedure to monitor numerous strains and substrates simultaneously.     

Alternatives to arginine as energy sources for the non-fermentative Mycoplasma gallinarum

Abstract In contrast to previously studied non-fermentative arginine-hydrolysing (F-/A+) Mycoplasma species, M. gallinarum cells suspended in salts solution oxidised ethanol and L-lactic, pyruvic and 2-oxobutyric acids. The organic acids were additionally shown effectively to replace arginine as energy sources in growth media. However, their presence did not inhibit arginine hydrolysis, nor did arginine inhibit organic acid catabolism. The ability to oxidase organic acids is a potentially useful diagnostic character enabling sub-division of the F-/A+ Mycoplasma species. M. gallinarum also differed from previously studied F-/A+ mycoplasmas in possessing relatively high NADH oxidase activity and producing H₂O₂ as only a minor product of NADH oxidation.     

Biochemical diversity of Mycoplasma fermentans strains

In this study, the metabolism of a diverse range of Mycoplasma fermentans strains was investigated. It was shown that the ability to utilise glucose, fructose and N-acetylglucosamine differentiated strains, and that the patterns and kinetics of substrate utilisation were correlated with the site of isolation, i.e. joint fluid, respiratory tract, urinary tract or cell culture. Interestingly, isolates from the urogenital tract of AIDS patients used fructose in preference to glucose. There was also some correlation of fructose and N-acetylglucosamine utilisation of isolates with M. fermentans sub-groups, identified in an independent study, and based on the distribution of insertion sequence-like elements in the M. fermentans genome.     

支原体菌株低温保存活力稳定性研究

目的研究低温冻存时间及温度对支原体菌种保存稳定性和菌种活力的影响。方法用固体平板计数法计算不同冻存时间、温度下的口腔支原体、肺炎支原体菌落数差异,分析这2个因素对口腔支原体、肺炎支原体菌种活力的影响。结果口腔支原体在生长48 h后达到生长高峰,肺炎支原体生长较为缓慢,在103 h到达生长高峰。口腔支原体在-70℃冻存1个月时,菌落数由10¹² cfu/mL下降至10¹¹ cfu/mL,冻存1个月的菌落数和冻存3个月、12个月的菌落数比较,差异均无统计学意义(P>0.05)。肺炎支原体在-70℃的冻存条件下,菌落数一直处于稳定水平;比较-35℃与-70℃的冻存条件下肺炎支原体的菌落数,差异无统计学意义(P>0.05),口腔支原体在-70℃冻存条件下的菌种活力明显高于-35℃(P<0.05)。结论口腔支原体生长迅速,但对于储存温度的敏感性较高,肺炎支原体相较口腔支原体生长缓慢,停滞期较长,菌株对冻存温度和时间的敏感度较低,稳定性高。菌种冻存温度应选择较低温度,冻存周期在1年内较为稳定。     

Distribution of ecto 5'-nucleotidase on Mycoplasma species associated with arthritis

The enzyme ecto 5'-nucleotidase (5'N) was found to be active on 8/14 strains of Mycoplasma fermentans, K(m) (+/-S.D.) 3.8+/-2.8 microM 5'-AMP, and on the type strain of Mycoplasma pulmonis, K(m) 0.63 microM 5'-AMP. The six M. fermentans strains lacking 5'N activity were related by restriction fragment length polymorphism typing. At pH 8.5, the type strains of Mycoplasma arthritidis, Mycoplasma buccale and Ureaplasma urealyticum showed a relatively non-specific phosphatase activity against 5'-AMP but no activity was shown by the type strains of Mycoplasma genitalium, Mycoplasma hominis, Mycoplasma orale, Mycoplasma penetrans, Mycoplasma pneumoniae and Mycoplasma salivarium at this pH. M. fermentans has been reported from rheumatoid joints, which show a raised 5'N activity on their synovial cells and in their fluid which may be associated directly or indirectly with the mycoplasma.     

A 41-kDa variable surface protein of Mycoplasma gallisepticum has a counterpart in Mycoplasma imitans and Mycoplasma iowae

Abstract Mycoplasma gallisepticun, M. imitans and M. iowae are three morphologically similar avian Mycoplasma species, and M. gallisepticum and M. imitans have been shown to be antigenically related. Using a monoclonal antibody that binds to the previously described size- and phase-variant integral membrane surface protein PvpA of M. gallisepticum , we have identified in all three avian Mycoplasma species a 41-kDa surface antigen, which in M. gallisepticum and M. imitans was identified as peripheral membrane protein undergoing variation in expression among clonal isolates. Southern blot analysis using the pvpA gene as a probe demonstrated sequence homology with M. imitans and M. iowae genomic DNA and suggested that a pvpA -related gene that may encode the 41-kDa product exists in these two Mycoplasma species. These studies establish (i) that M. iowae is antigenically related to M. gallisepticum and M. imitans , (ii) that the three species share non-ribosomal gene sequences, and (iii) that peripheral membrane proteins contribute to Mycoplasma surface variation.     

猪气喘病实验猪模型的建立

目的 研究建立猪气喘病人工发病模型。方法 将分离得到的一株猪肺炎支原体(Mycoplasma hyopneumoniae,Mhp)Js株进行各种试验鉴定,证实其为Mhp强毒株。每头猪肺内接种Js株培养物2ml,15～25d后观察临床症状和病理变化,采集病变组织,经冻干制成攻毒用组织毒。安检合格,批号为20000324。给15头小梅山二元杂交猪分别气管内注射以KM₂培养基作10^-2、10^-3、10^-4和10^-5稀释的强毒,每头猪5ml,对照组注射培养基。攻毒后25d观察试验猪临诊症状,X线透视,记录病理变化。结果 10^-2、10^-3、10^-4稀释的强毒试验组猪均出现了典型的猪气喘病临床症状和病理变化。结论 人工发病试验测得Mhp Js株组织强毒接种气管内注射最小发病剂量为10^-4稀释5ml,正式试验人工发病可用100个最小发病剂量即强毒冻干物1:100稀释气管内注射5ml,可确保攻毒成功。     

Chemotaxis away from thiocyanic and isothiocyanic esters in Pseudomonas aeruginosa

Abstract A novel mycoplasmal species designated as Mycoplasma penetrans has recently been isolated from patients infected with human immunodeficiency virus. The 16S rRNA gene from this mycoplasma was cloned and its nucleotide sequence determined. This sequence was aligned with previously published homologous sequences from several mycoplasmas and with related Gram-positive bacteria and a phylogenetic tree was constructed. The results indicate that M. penetrans belongs to the evolutionary group Pneumoniae.     

A chromosomal region of Mycoplasma agalactiae containing vsp-related genes undergoes in vivo rearrangement in naturally infected animals

A Mycoplasma agalactiae genomic fragment carrying four vsp-related genes (designated avg: agalactiae variable genes) was cloned, sequenced and compared to the vspA gene of Mycoplasma bovis. The following features were revealed: (i) the presence of a highly conserved vsp 5' upstream region; (ii) a highly homologous vsp N-terminal end encoding a putative lipoprotein signal sequence; (iii) sequence divergence of the rest of the mature proteins. By using avg specific probes in Southern blot analysis of genomic DNAs of M. agalactiae strains as well as of isolates from infected animals, marked DNA polymorphism of avg fragments was demonstrated. In addition, the avg genomic fingerprints were monitored for a period of 7 months, in isolates of M. agalactiae from an individual chronically infected animal. The results provided evidence that a chromosomal region of M. agalactiae, carrying vsp-related genes, undergoes rearrangements in vivo in the natural animal host during the course of infection.     

Development of two PCR assays for the identification of mycoplasmas causing contagious agalactia

Abstract A new detection test for the mycoplasmas causing contagious agalactia, Mycoplasma agalactiae , M. capricolum subsp. capricolum and M. mycoides subsp. mycoldes L.C., was developed. It was based on two polymerase chain reaction assays: the Ma-PCR for the detection of M. agalactiae and the MYC-PCR for the 'mycoides cluster' thus including M. capricolum subsp. capricolum and M. mycoides subsp. mycoides L.C. An M. agalactiae strain was identified by a 933-bp Ma-PCR product and no amplification with the MYC-PCR. In contrast, a 460-bp MYC-PCR product and a negative or a 350-bp Ma-PCR product characterized a 'mycoides cluster' strain. M. capricolum subsp. capricolum and M. mycoides subsp. mycoides L.C. were identified by their species-specific Asel pattern of the 460-bp MYC-PCR product.     

常见支原体感染误诊与对策

临床支原体感染易发生误诊,不但加重患者精神和经济负担,而且延误患者病情,甚至留下后遗症。为此,我们综述了常见支原体感染误诊的特点和原因,深挖其中思维和思想根源,探讨减少或避免该类误诊现象的策略,旨在为临床医护人员和检验技术人员提供参考建议。     

PCR技术在鼠肺支原体检测中应用的初步研究

目的　探讨PCR技术在鼠肺支原体检测中的应用,希望能建立一种可行、快速、敏感的检测方法。方法　使用支原体通用引物及鼠肺支原体特异性引物对14 份大鼠喉气管拭子洗液和拭子支原体培养液进行PCR扩增,2 % 琼脂糖电泳鉴定。另设M53 和ATCC19612 二株标准鼠肺支原体菌株作阳性对照。结果　通用引物对大鼠喉气管拭子洗液检出率8/14 ,拭子支原体培养液检出率14/14,鼠肺支原体特异引物PCR扩增对大鼠喉气管拭子洗液检出率0/14 ,拭子支原体培养液3/14。通用引物扩增M53 和ATCC19612 二株标准株均呈现阳性,而鼠肺支原体特异引物扩增M53 和ATCC19612,只有M53 呈现阳性。结论　PCR通用引物检测比普通分离培养省时省力,而我们采用国外某学者认为对鼠肺支原体有特异性的引物,是否可用于鼠肺支原体的特异性PCR 检查仍需进一步探讨。     

细胞培养中支原体污染的PCR检测

根据支原体16s rDNA序列,选择RemyTeyssou设计的三条寡核苷酸链,组成两套引物:P_(1-2a)能检测出细胞培养中常见的各种支原体,P_(1-2b)能检出无胆甾原体。反应可检出体系中10CFV的菌体。此法先用于对实验室人为污染支原体Vero细胞的检测,后与DNA 染色法和培养法比较,检测了49份生物样品,其中24份传代细胞,PCR检测的阳性率为58％,DNA染色法为42％,培养法为33％;三者的灵敏性比较,PCR可检出10~(-3)稀释度的阳性样品,高于其他两种方法。此PCR方法快速、灵敏、特异,适用于细胞培养中支原体污染的检测。     

Metal-induced extracellular protein excretion in Arthrobacter aurescens

Abstract Mycoplasma contamination of cell cultures is a menace to diagnostic and research procedures. Rapid and reliable detection methods are, therefore, sorely needed. After comparing 16S rRNA sequences from those mycoplasmas that contaminate cell cultures, three different oligonucleotide probes were constructed. Two of these probes were designed to be group-specific and one to be species-specific. The three oligonucleotide probes were designed to cover all mycoplasmas commonly isolated from cell cultures. Contaminated cell lines could easily be detected by a direct filter hybridization assay in which the probes were incubated jointly. The assay proved to be rapid and sensitive with the possibility to perform and evaluate the mycoplasma testing within one working day.     

Two cholesterol pools in Acholeplasma laidlawii membranes

Cholesterol exchange kinetics between [14C]cholesterol-labeled Acholeplasma laidlawii and Mycoplasma gallisepticum cells and phosphatidylcholine-cholesterol vesicles followed a biphasic curve, with faster exchange rates for A. laidlawii. The same biphasic curve was obtained with isolated membranes. Cholesterol exchange between lipid vesicles and A. laidlawii cells depleted of phospholipids by phospholipase A2, fitted a monophasic linear curve. The data support the hypothesis that the biphasic cholesterol exchange kinetics do not result from the transbilayer distribution of cholesterol, but reflect the presence in the membrane of two cholesterol pools associated with lipids of high and low affinity for cholesterol.     

女性生殖道炎症支原体多重耐药性分析

了解本地区在采用常规抗生素治疗支原体后多重耐药株的产生情况,为临床针对性用药提供科学依据。采用培养法对女性生殖道炎患者分泌物进行支原体培养、体外药敏试验及分析。结果可见,感染数量≥10~4 cfu/mL的支原体阳性率为52.9%(82/155);13种抗生素中,耐药种数构成比为6R>2R、4R、5R>3R>1R>8R>7R、10R>0R>9R、12R、13R;耐药率为林可霉素>壮观霉素>环丙沙星>诺氟沙星>司帕沙星>罗红霉素>氧氟沙星>克拉霉素>左氧氟沙星>阿齐霉素>强力霉素,美满霉素>交沙霉素。体外药敏试验对临床治疗支原体感染及减少多重耐药株的产生具有重要指导意义。     

Adherence of Pathogenic Mycoplasmas to Host Cells

The significant genome compaction in mycoplasmas was made possible by adoption of a parasitic lifestyle. During their evolution and adaptation to a parasitic mode of life the mycoplasmas have developed various genetic systems enabling their attachment to host tissues as well as a highly plastic set of variable surface proteins. The generation of a versatile surface coat through high-frequency phase and size variation provides the organism with a useful tool for immune system avoidance, allowing the mycoplasmas to escape antibody attack, explaining why these minute organisms are such successful parasites.