鼠疫耶尔森氏菌噬菌体Yep-phi基因组研究及其受体鉴定
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摘要
鼠疫的病原是鼠疫耶尔森氏菌（Yersinia pestis,简称鼠疫菌），属于肠杆菌科耶尔森氏菌属。鼠疫在历史上曾经引发三次世界范围的鼠疫大流行，给人类带来巨大的灾难。2000年，世界卫生组织已经将鼠疫列为重新抬头的传染病。鼠疫菌是传统的生物战剂，同时还是国际恐怖分子可能用于制造生物恐怖的首选微生物之一。鼠疫对于人类健康仍然是一个巨大的威胁，尤其是败血症鼠疫和肺鼠疫，若未及时治疗，通常是致命的。抗生素治疗（例如四环素和链霉素）被WHO专家委员会认为是治疗鼠疫的“金标准”，然而，耐药性鼠疫菌的出现给我们敲响了警钟，需要研制能够替代抗生素的方案。1995年在腺鼠疫患者体内分离到了第一株多重耐药鼠疫菌株,该菌株携带了能够抵抗12种抗生素（包括所有用于鼠疫预防和治疗的抗生素）的耐药基因。鼠疫菌噬菌体（bacteriophage）因对宿主的高度特异性和敏感性，对临床诊断和流行病学调查具有重要意义。随着多重耐药（multidrug resistant）鼠疫菌株的出现，噬菌体有可能成为预防和治疗鼠疫菌感染的抗生素替代品。
Yep-phi是在中国分离的，常规用于鼠疫菌诊断的噬菌体，在不同温度下均能特异裂解鼠疫菌，在分类地位上属于T7噬菌体家族。Yep-phi的壳体由二十面体对称的头部和尾部组成，头部和尾部通过颈部相连。本研究对Yep-phi进行了全基因组序列的测定（序列登录号：HQ333270）和蛋白质组鉴定，Yep-phi基因组长度为38,611bp，含有217bp的末端重复，GC含量47.12mol%，与宿主鼠疫菌（47.6mol%）相似。共编码45个ORF。并与已测序的同属T7家族的鼠疫菌噬菌体PhiA1122（序列登录号：AY247822）、Berlin（序列登录号：AM183667）和Yepe2（序列登录号：EU734170）进行了比较基因组学分析。结果提示这4株烈性噬菌体可以明显分为两个亚群：Yep-phi亚群（Yep-phi、Berlin和Yepe2）和PhiA1122亚群（PhiA1122）。同源重组是近缘噬菌体的在进化过程中的重要机制，在Yep-phi亚群中预测到四个重组事件，说明这三株噬菌体在进化上是密切相关的。
噬菌体裂解细菌的特异性主要取决于噬菌体与细菌细胞壁上特异性受体的相互识别与吸附。了解噬菌体受体结合蛋白与受体的结构功能有助于理解受体识别机制，进一步理解引发感染的后续步骤。目前已经鉴定出八株鼠疫菌噬菌体的受体（L-413C、P2vir1、PhiJA1、PhiA1122、Pokrovskaya、T7Yp、Y和PST），分别位于LPS的不同位置，这八株噬菌体包含了已经测序的PhiA1122和L-413C噬菌体。Yep-phi是T7类噬菌体，已鉴定的T7类噬菌体（例如T7、T3、PhiA1122、PhiYeO3-12）也都是以LPS为受体的。
本研究以噬菌体Yep-phi为对象，鉴定了噬菌体受体结合蛋白与受体，通过噬菌体吸附实验、噬菌斑实验、亲和层析和Western Blotting实验，证实了除了鼠疫菌的LPS之外，外膜蛋白OmpF和Ail也是噬菌体受体，并评价了鼠疫菌受体突变株与回补株的裂解效率，鉴定了相互作用的结构域和介导相互作用的关键氨基酸。尾丝蛋白gp17第510-529位氨基酸是介导相互作用的结构域，尾丝蛋白518N、519N、523S是识别OmpF的关键位点，而518N、519N、522C和523S是识别Ail的关键位点。本研究首次鉴定了外膜蛋白可作为T7类噬菌体的受体。而Yep-phi受体与其它T7类噬菌体的差别是由尾丝蛋白的序列特异性所决定的，这项工作证实了尾丝蛋白在进化中和多样的噬菌体系统中的重要性，同时对于发展噬菌体治疗鼠疫菌感染和鉴定鼠疫菌的技术以及理解噬菌体与细菌的相互作用具有重要意义。
Yersinia pestis, the causative agent of plague, belongs to the familyEnterobacteriaceae genus Yersinia. Yersinia pestis has killed hundreds of millions ofpeople in the three major historical plague pandemics. The World HealthOrganization (WHO) has classified plague as a re-emerging infectious disease in2000.Y. pestis has gained much attention as a possible biowarfare agent that could bemisused by bioterrorists. Plague still poses a significant threat to human health. Thesepticaemic and pneumonic forms are always lethal if untreated in time. The use ofantibiotics such as streptomycin and tetracycline for treating plague has beenembraced by the World Health Organization Expert Committee on Plague as the 'goldstandard' treatment scheme. However, concerns regarding the development ofantibiotic-resistant Y. pestis strains have led to the exploration of alternatives toantibiotics. In1995, multiple drug-resistant strains of Y. pestis have been isolatedfrom patients with bubonic plague. One of them carried genes of high-level resistanceto12antibiotics, including virtually all of the drugs commonly used for plagueprophylaxis and treatment. Y. pestis phages play an important role in clinicaldiagnosis and epidemiological investigation due to their high specificity andsensitivity to its host. With the emergence of multiple drug-resistant Yersinia pestis,phages could be used as alternatives to antibiotics for the prevention and treatment ofplague.
Yep-phi, a lytic phage of Y. pestis and a member of the T7family, was isolatedin China and is routinely used as a diagnostic phage for the identification of theplague pathogen. Yep-phi infects Y. pestis grown at both20°C and37°C, and isinactive in other Yersinia species irrespective of the growth temperature. Yep-phi hasan isometric hexagonal head containing dsDNA and a short non-contractile conicaltail. In this study, we sequenced the Yep-phi genome (GenBank accession no.HQ333270) and performed proteomics analysis. The genome consists of38,611bp ofDNA, including direct terminal repeats of217bp, and is predicted to contain45ORFs.The G+C content of the Yep-phi genome is47.12%, similar to that (47.6%) of itshost Y. pestis. Compared with the three available genome sequences of lytic phagesfor Y. pestis, the phages could be divided into two subgroups. Yep-phi displaysmarked homology to the bacteriophages Berlin (GenBank accession no. AM183667)and Yepe2(GenBank accession no. EU734170), and these comprise one subgroup.The other subgroup is represented by bacteriophage PhiA1122(GenBank accession no. AY247822). Homologous recombination is a powerful source of geneticvariability and a potent evolutionary mechanism for closely related bacteriophages.Recombination analysis detected four potential recombination events in the Yep-phisubgroup.
Phage’s host specificity depends largely on the recognition and adsorption of thephage to its host surface receptors. Therefore, it is critical to understand the process ofphage lysis by exploring the mechanism of phage-receptor interactions. The receptorsof eight Y. pestis phages have been identified (L-413C, P2vir1, PhiJA1, PhiA1122,Pokrovskaya, T7Yp, Y and PST). All these phages employ different components oflipopolysaccharide (LPS) as a specific receptor. As far as we know, all closely relatedT7-like phages (T7, T3, PhiA1122and PhiYeO3-12) utilize the LPS core as theirreceptors.
In this study, the phage receptor-binding protein and its receptors were identifiedfor Y. pestis diagnostic phage Yep-phi. Based on phage adsorption, phage plaqueformation, affinity chromatography and Western Blotting assays, the outer membraneproteins of Y. pestis, namely, Ail and OmpF, were identified to act as the receptors ofYep-phi in addition to the rough lipopolysaccharide. The plaguing efficiencies ofphage were evaluated on Yersinia pestis mutants of deleting different potentialreceptor genes singly or in different combinations and their trans-complementedstrains; and the necessary domains responsible for the interactions were identified andvalidated for phage tail fiber protein. The510-529residues of the distal portion of thephage tail fiber protein were sufficient in allowing binding to the OMP receptors invitro. Residues518N,519N, and523S of this protein are essential for the interactionwith OmpF, whereas residues518N,519N,522C, and523S are essential for theinteraction with Ail. This study is the first to demonstrate membrane-bound proteinsto act as receptors for a T7-related bacteriophage. Yep-phi has a unique hostspecificity that can be attributed to its tail fiber gp17protein. The observationshighlight the importance of the tail fiber protein in the evolution and function ofvarious complex phage systems. These findings are critical in developing phage-basedtherapeutic strategy to treat Y. pestis infection and diagnostic agent for identifying Y.pestis, and in providing insights into phage-bacterium interaction.
Yep-phi是在中国分离的，常规用于鼠疫菌诊断的噬菌体，在不同温度下均能特异裂解鼠疫菌，在分类地位上属于T7噬菌体家族。Yep-phi的壳体由二十面体对称的头部和尾部组成，头部和尾部通过颈部相连。本研究对Yep-phi进行了全基因组序列的测定（序列登录号：HQ333270）和蛋白质组鉴定，Yep-phi基因组长度为38,611bp，含有217bp的末端重复，GC含量47.12mol%，与宿主鼠疫菌（47.6mol%）相似。共编码45个ORF。并与已测序的同属T7家族的鼠疫菌噬菌体PhiA1122（序列登录号：AY247822）、Berlin（序列登录号：AM183667）和Yepe2（序列登录号：EU734170）进行了比较基因组学分析。结果提示这4株烈性噬菌体可以明显分为两个亚群：Yep-phi亚群（Yep-phi、Berlin和Yepe2）和PhiA1122亚群（PhiA1122）。同源重组是近缘噬菌体的在进化过程中的重要机制，在Yep-phi亚群中预测到四个重组事件，说明这三株噬菌体在进化上是密切相关的。
噬菌体裂解细菌的特异性主要取决于噬菌体与细菌细胞壁上特异性受体的相互识别与吸附。了解噬菌体受体结合蛋白与受体的结构功能有助于理解受体识别机制，进一步理解引发感染的后续步骤。目前已经鉴定出八株鼠疫菌噬菌体的受体（L-413C、P2vir1、PhiJA1、PhiA1122、Pokrovskaya、T7Yp、Y和PST），分别位于LPS的不同位置，这八株噬菌体包含了已经测序的PhiA1122和L-413C噬菌体。Yep-phi是T7类噬菌体，已鉴定的T7类噬菌体（例如T7、T3、PhiA1122、PhiYeO3-12）也都是以LPS为受体的。
本研究以噬菌体Yep-phi为对象，鉴定了噬菌体受体结合蛋白与受体，通过噬菌体吸附实验、噬菌斑实验、亲和层析和Western Blotting实验，证实了除了鼠疫菌的LPS之外，外膜蛋白OmpF和Ail也是噬菌体受体，并评价了鼠疫菌受体突变株与回补株的裂解效率，鉴定了相互作用的结构域和介导相互作用的关键氨基酸。尾丝蛋白gp17第510-529位氨基酸是介导相互作用的结构域，尾丝蛋白518N、519N、523S是识别OmpF的关键位点，而518N、519N、522C和523S是识别Ail的关键位点。本研究首次鉴定了外膜蛋白可作为T7类噬菌体的受体。而Yep-phi受体与其它T7类噬菌体的差别是由尾丝蛋白的序列特异性所决定的，这项工作证实了尾丝蛋白在进化中和多样的噬菌体系统中的重要性，同时对于发展噬菌体治疗鼠疫菌感染和鉴定鼠疫菌的技术以及理解噬菌体与细菌的相互作用具有重要意义。
Yersinia pestis, the causative agent of plague, belongs to the familyEnterobacteriaceae genus Yersinia. Yersinia pestis has killed hundreds of millions ofpeople in the three major historical plague pandemics. The World HealthOrganization (WHO) has classified plague as a re-emerging infectious disease in2000.Y. pestis has gained much attention as a possible biowarfare agent that could bemisused by bioterrorists. Plague still poses a significant threat to human health. Thesepticaemic and pneumonic forms are always lethal if untreated in time. The use ofantibiotics such as streptomycin and tetracycline for treating plague has beenembraced by the World Health Organization Expert Committee on Plague as the 'goldstandard' treatment scheme. However, concerns regarding the development ofantibiotic-resistant Y. pestis strains have led to the exploration of alternatives toantibiotics. In1995, multiple drug-resistant strains of Y. pestis have been isolatedfrom patients with bubonic plague. One of them carried genes of high-level resistanceto12antibiotics, including virtually all of the drugs commonly used for plagueprophylaxis and treatment. Y. pestis phages play an important role in clinicaldiagnosis and epidemiological investigation due to their high specificity andsensitivity to its host. With the emergence of multiple drug-resistant Yersinia pestis,phages could be used as alternatives to antibiotics for the prevention and treatment ofplague.
Yep-phi, a lytic phage of Y. pestis and a member of the T7family, was isolatedin China and is routinely used as a diagnostic phage for the identification of theplague pathogen. Yep-phi infects Y. pestis grown at both20°C and37°C, and isinactive in other Yersinia species irrespective of the growth temperature. Yep-phi hasan isometric hexagonal head containing dsDNA and a short non-contractile conicaltail. In this study, we sequenced the Yep-phi genome (GenBank accession no.HQ333270) and performed proteomics analysis. The genome consists of38,611bp ofDNA, including direct terminal repeats of217bp, and is predicted to contain45ORFs.The G+C content of the Yep-phi genome is47.12%, similar to that (47.6%) of itshost Y. pestis. Compared with the three available genome sequences of lytic phagesfor Y. pestis, the phages could be divided into two subgroups. Yep-phi displaysmarked homology to the bacteriophages Berlin (GenBank accession no. AM183667)and Yepe2(GenBank accession no. EU734170), and these comprise one subgroup.The other subgroup is represented by bacteriophage PhiA1122(GenBank accession no. AY247822). Homologous recombination is a powerful source of geneticvariability and a potent evolutionary mechanism for closely related bacteriophages.Recombination analysis detected four potential recombination events in the Yep-phisubgroup.
Phage’s host specificity depends largely on the recognition and adsorption of thephage to its host surface receptors. Therefore, it is critical to understand the process ofphage lysis by exploring the mechanism of phage-receptor interactions. The receptorsof eight Y. pestis phages have been identified (L-413C, P2vir1, PhiJA1, PhiA1122,Pokrovskaya, T7Yp, Y and PST). All these phages employ different components oflipopolysaccharide (LPS) as a specific receptor. As far as we know, all closely relatedT7-like phages (T7, T3, PhiA1122and PhiYeO3-12) utilize the LPS core as theirreceptors.
In this study, the phage receptor-binding protein and its receptors were identifiedfor Y. pestis diagnostic phage Yep-phi. Based on phage adsorption, phage plaqueformation, affinity chromatography and Western Blotting assays, the outer membraneproteins of Y. pestis, namely, Ail and OmpF, were identified to act as the receptors ofYep-phi in addition to the rough lipopolysaccharide. The plaguing efficiencies ofphage were evaluated on Yersinia pestis mutants of deleting different potentialreceptor genes singly or in different combinations and their trans-complementedstrains; and the necessary domains responsible for the interactions were identified andvalidated for phage tail fiber protein. The510-529residues of the distal portion of thephage tail fiber protein were sufficient in allowing binding to the OMP receptors invitro. Residues518N,519N, and523S of this protein are essential for the interactionwith OmpF, whereas residues518N,519N,522C, and523S are essential for theinteraction with Ail. This study is the first to demonstrate membrane-bound proteinsto act as receptors for a T7-related bacteriophage. Yep-phi has a unique hostspecificity that can be attributed to its tail fiber gp17protein. The observationshighlight the importance of the tail fiber protein in the evolution and function ofvarious complex phage systems. These findings are critical in developing phage-basedtherapeutic strategy to treat Y. pestis infection and diagnostic agent for identifying Y.pestis, and in providing insights into phage-bacterium interaction.
引文
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39. Kemp P, Gupta M, Molineux IJ: Bacteriophage T7DNA ejection into cells isinitiated by an enzyme-like mechanism. Molecular microbiology2004,53(4):1251-1265.
40. Steven AC, Trus BL, Maizel JV, Unser M, Parry DA, Wall JS, Hainfeld JF,Studier FW: Molecular substructure of a viral receptor-recognition protein.The gp17tail-fiber of bacteriophage T7. Journal of molecular biology1988,200(2):351-365.
41. Wang IN, Smith DL, Young R: Holins: the protein clocks of bacteriophageinfections. Annual review of microbiology2000,54:799-825.
42. Young I, Wang I, Roof WD: Phages will out: strategies of host cell lysis.Trends in microbiology2000,8(3):120-128.
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44.张京云: El Tor型霍乱弧菌分型噬菌体VP3的感染受体与基因转录时序研究.博士.中国疾病预防控制中心;2008.
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46. Kolodziejek AM, Hovde CJ, Minnich SA: Yersinia pestis Ail: multiple rolesof a single protein. Frontiers in cellular and infection microbiology2012,2:103.
47. Lindberg AA: Bacteriophage receptors. Annual review of microbiology1973,27:205-241.
48. Skurnik M: Yersinia surface structures and bacteriophages. Advances inexperimental medicine and biology2012,954:293-301.
49. Sao-Jose C, Baptista C, Santos MA: Bacillus subtilis operon encoding amembrane receptor for bacteriophage SPP1. Journal of bacteriology2004,186(24):8337-8346.
50. Feiss M, Widner W, Miller G, Johnson G, Christiansen S: Structure of thebacteriophage lambda cohesive end site: location of the sites of terminasebinding (cosB) and nicking (cosN). Gene1983,24(2-3):207-218.
51. Maluf NK, Yang Q, Catalano CE: Self-association properties of thebacteriophage lambda terminase holoenzyme: implications for the DNApackaging motor. Journal of molecular biology2005,347(3):523-542.
52. Koebnik R, Locher KP, Van Gelder P: Structure and function of bacterialouter membrane proteins: barrels in a nutshell. Molecular microbiology2000,37(2):239-253.
53. Shin H, Lee JH, Kim H, Choi Y, Heu S, Ryu S: Receptor diversity and hostinteraction of bacteriophages infecting Salmonella enterica serovarTyphimurium. PLoS One2012,7(8):e43392.
54. Garcia-Doval C, van Raaij MJ: Structure of the receptor-bindingcarboxy-terminal domain of bacteriophage T7tail fibers. Proc Natl AcadSci U S A2012,109(24):9390-9395.
55. Kruger DH, Schroeder C: Bacteriophage T3and bacteriophage T7virus-host cell interactions. Microbiological reviews1981,45(1):9-51.
56. Li Y, Gao H, Qin L, Li B, Han Y, Guo Z, Song Y, Zhai J, Du Z, Wang X et al:Identification and characterization of PhoP regulon members in Yersiniapestis biovar Microtus. BMC genomics2008,9:143.
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59. Radding CM: The role of exonuclease and beta protein of bacteriophagelambda in genetic recombination. I. Effects of red mutants on proteinstructure. Journal of molecular biology1970,52(3):491-499.
60. Passy SI, Yu X, Li Z, Radding CM, Egelman EH: Rings and filaments ofbeta protein from bacteriophage lambda suggest a superfamily ofrecombination proteins. Proc Natl Acad Sci U S A1999,96(8):4279-4284.
61. Li Z, Karakousis G, Chiu SK, Reddy G, Radding CM: The beta protein ofphage lambda promotes strand exchange. Journal of molecular biology1998,276(4):733-744.
62. Poteete AR, Fenton AC, Murphy KC: Modulation of Escherichia coliRecBCD activity by the bacteriophage lambda Gam and P22Abcfunctions. Journal of bacteriology1988,170(5):2012-2021.
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68. Gibbs KA, Isaac DD, Xu J, Hendrix RW, Silhavy TJ, Theriot JA: Complexspatial distribution and dynamics of an abundant Escherichia coli outermembrane protein, LamB. Molecular microbiology2004,53(6):1771-1783.
69. Nikaido H: Molecular basis of bacterial outer membrane permeabilityrevisited. Microbiology and molecular biology reviews: MMBR2003,67(4):593-656.
70. Schirmer T, Keller TA, Wang YF, Rosenbusch JP: Structural basis for sugartranslocation through maltoporin channels at3.1A resolution. Science1995,267(5197):512-514.
71. Bekhit A, Fukamachi T, Saito H, Kobayashi H: The role of OmpC andOmpF in acidic resistance in Escherichia coli. Biological&pharmaceuticalbulletin2011,34(3):330-334.
72. Krishnan S, Prasadarao NV: Outer membrane protein A and OprF:versatile roles in Gram-negative bacterial infections. The FEBS journal2012,279(6):919-931.
73. Yamashita S, Lukacik P, Barnard TJ, Noinaj N, Felek S, Tsang TM, KrukonisES, Hinnebusch BJ, Buchanan SK: Structural insights into Ail-mediatedadhesion in Yersinia pestis. Structure2011,19(11):1672-1682.
74. Kolodziejek AM, Schnider DR, Rohde HN, Wojtowicz AJ, Bohach GA,Minnich SA, Hovde CJ: Outer membrane protein X (Ail) contributes toYersinia pestis virulence in pneumonic plague and its activity is dependenton the lipopolysaccharide core length. Infect Immun2010,78(12):5233-5243.
75. Bartra SS, Styer KL, O'Bryant DM, Nilles ML, Hinnebusch BJ, Aballay A,Plano GV: Resistance of Yersinia pestis to complement-dependent killing ismediated by the Ail outer membrane protein. Infect Immun2008,76(2):612-622.
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37.洪健,周雪平: ICTV第八次报告的最新病毒分类系统. Virologica Sinica2006(01):84-96.
38. Letellier L, Boulanger P, de Frutos M, Jacquot P: Channeling phage DNAthrough membranes: from in vivo to in vitro. Research in microbiology2003,154(4):283-287.
39. Kemp P, Gupta M, Molineux IJ: Bacteriophage T7DNA ejection into cells isinitiated by an enzyme-like mechanism. Molecular microbiology2004,53(4):1251-1265.
40. Steven AC, Trus BL, Maizel JV, Unser M, Parry DA, Wall JS, Hainfeld JF,Studier FW: Molecular substructure of a viral receptor-recognition protein.The gp17tail-fiber of bacteriophage T7. Journal of molecular biology1988,200(2):351-365.
41. Wang IN, Smith DL, Young R: Holins: the protein clocks of bacteriophageinfections. Annual review of microbiology2000,54:799-825.
42. Young I, Wang I, Roof WD: Phages will out: strategies of host cell lysis.Trends in microbiology2000,8(3):120-128.
43.刘平:分枝杆菌噬菌体的生物学特性及基因组学研究.博士.重庆医科大学;2012.
44.张京云: El Tor型霍乱弧菌分型噬菌体VP3的感染受体与基因转录时序研究.博士.中国疾病预防控制中心;2008.
45. Catalano CE: The terminase enzyme from bacteriophage lambda: aDNA-packaging machine. Cellular and molecular life sciences: CMLS2000,57(1):128-148.
46. Kolodziejek AM, Hovde CJ, Minnich SA: Yersinia pestis Ail: multiple rolesof a single protein. Frontiers in cellular and infection microbiology2012,2:103.
47. Lindberg AA: Bacteriophage receptors. Annual review of microbiology1973,27:205-241.
48. Skurnik M: Yersinia surface structures and bacteriophages. Advances inexperimental medicine and biology2012,954:293-301.
49. Sao-Jose C, Baptista C, Santos MA: Bacillus subtilis operon encoding amembrane receptor for bacteriophage SPP1. Journal of bacteriology2004,186(24):8337-8346.
50. Feiss M, Widner W, Miller G, Johnson G, Christiansen S: Structure of thebacteriophage lambda cohesive end site: location of the sites of terminasebinding (cosB) and nicking (cosN). Gene1983,24(2-3):207-218.
51. Maluf NK, Yang Q, Catalano CE: Self-association properties of thebacteriophage lambda terminase holoenzyme: implications for the DNApackaging motor. Journal of molecular biology2005,347(3):523-542.
52. Koebnik R, Locher KP, Van Gelder P: Structure and function of bacterialouter membrane proteins: barrels in a nutshell. Molecular microbiology2000,37(2):239-253.
53. Shin H, Lee JH, Kim H, Choi Y, Heu S, Ryu S: Receptor diversity and hostinteraction of bacteriophages infecting Salmonella enterica serovarTyphimurium. PLoS One2012,7(8):e43392.
54. Garcia-Doval C, van Raaij MJ: Structure of the receptor-bindingcarboxy-terminal domain of bacteriophage T7tail fibers. Proc Natl AcadSci U S A2012,109(24):9390-9395.
55. Kruger DH, Schroeder C: Bacteriophage T3and bacteriophage T7virus-host cell interactions. Microbiological reviews1981,45(1):9-51.
56. Li Y, Gao H, Qin L, Li B, Han Y, Guo Z, Song Y, Zhai J, Du Z, Wang X et al:Identification and characterization of PhoP regulon members in Yersiniapestis biovar Microtus. BMC genomics2008,9:143.
57. Parker CE, Warren MR, Mocanu V: Mass Spectrometry for Proteomics.
58. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B,Bangham R, Benito R, Boeke JD, Bussey H et al: Functionalcharacterization of the S. cerevisiae genome by gene deletion and parallelanalysis. Science1999,285(5429):901-906.
59. Radding CM: The role of exonuclease and beta protein of bacteriophagelambda in genetic recombination. I. Effects of red mutants on proteinstructure. Journal of molecular biology1970,52(3):491-499.
60. Passy SI, Yu X, Li Z, Radding CM, Egelman EH: Rings and filaments ofbeta protein from bacteriophage lambda suggest a superfamily ofrecombination proteins. Proc Natl Acad Sci U S A1999,96(8):4279-4284.
61. Li Z, Karakousis G, Chiu SK, Reddy G, Radding CM: The beta protein ofphage lambda promotes strand exchange. Journal of molecular biology1998,276(4):733-744.
62. Poteete AR, Fenton AC, Murphy KC: Modulation of Escherichia coliRecBCD activity by the bacteriophage lambda Gam and P22Abcfunctions. Journal of bacteriology1988,170(5):2012-2021.
63. Chaveroche MK, Ghigo JM, d'Enfert C: A rapid method for efficient genereplacement in the filamentous fungus Aspergillus nidulans. Nucleic acidsresearch2000,28(22):E97.
64. Rose RE: The nucleotide sequence of pACYC184. Nucleic acids research1988,16(1):355.
65. Mosoyan G, Nagi C, Marukian S, Teixeira A, Simonian A, Resnick-SilvermanL, Difeo A, Johnston D, Reynolds SR, Roses DF et al: Multiple BreastCancer Cell-Lines Derived from a Single Tumor Differ in Their MolecularCharacteristics and Tumorigenic Potential. PLoS One2013,8(1):25.
66. Sorensen MC, van Alphen LB, Fodor C, Crowley SM, Christensen BB,Szymanski CM, Brondsted L: Phase Variable Expression of CapsularPolysaccharide Modifications Allows Campylobacter jejuni to AvoidBacteriophage Infection in Chickens. Frontiers in cellular and infectionmicrobiology2012,2:11.
67. Zhou D, Han Y, Yang R: Molecular and physiological insights into plaguetransmission, virulence and etiology. Microbes Infect2006,8(1):273-284.
68. Gibbs KA, Isaac DD, Xu J, Hendrix RW, Silhavy TJ, Theriot JA: Complexspatial distribution and dynamics of an abundant Escherichia coli outermembrane protein, LamB. Molecular microbiology2004,53(6):1771-1783.
69. Nikaido H: Molecular basis of bacterial outer membrane permeabilityrevisited. Microbiology and molecular biology reviews: MMBR2003,67(4):593-656.
70. Schirmer T, Keller TA, Wang YF, Rosenbusch JP: Structural basis for sugartranslocation through maltoporin channels at3.1A resolution. Science1995,267(5197):512-514.
71. Bekhit A, Fukamachi T, Saito H, Kobayashi H: The role of OmpC andOmpF in acidic resistance in Escherichia coli. Biological&pharmaceuticalbulletin2011,34(3):330-334.
72. Krishnan S, Prasadarao NV: Outer membrane protein A and OprF:versatile roles in Gram-negative bacterial infections. The FEBS journal2012,279(6):919-931.
73. Yamashita S, Lukacik P, Barnard TJ, Noinaj N, Felek S, Tsang TM, KrukonisES, Hinnebusch BJ, Buchanan SK: Structural insights into Ail-mediatedadhesion in Yersinia pestis. Structure2011,19(11):1672-1682.
74. Kolodziejek AM, Schnider DR, Rohde HN, Wojtowicz AJ, Bohach GA,Minnich SA, Hovde CJ: Outer membrane protein X (Ail) contributes toYersinia pestis virulence in pneumonic plague and its activity is dependenton the lipopolysaccharide core length. Infect Immun2010,78(12):5233-5243.
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