Estimate of the genome size of various microorganisms

Getting Beyond the Toy Domain. Meditations on David Deamer's "Assembling Life"

David Deamer has written another book, Assembling Life, on the origin of life. It is unapologetically polemic, presenting Deamer's view that life originated in fresh water hydrothermal fields on volcanic islands on early Earth, arguing that this provided a unique environment not just for organic chemistry but for the self-assembling structure that drive that chemistry and form the basis of structure in life. It is worth reading, it is an advance in the field, but is it convincing? I argue that the Origin of Life field as a whole is unconvincing, generating results in Toy Domains that cannot be scaled to any real world scenario. I suggest that, by analogy with the history of artificial intelligence and solar astronomy, we need much more scale, and fundamentally new ideas, to take the field forward.

Improved Microfouling Assay Employing a DNA-Specific Fluorochrome and Polystyrene as Substratum

With a direct count assay, 10 fouling bacterial isolates have been characterized for their ability to adhere to glass cover slips and polystyrene dishes. Although most adhered in greater numbers to polystyrene, the preference was statistically significant for only seven isolates at the 95% confidence level, due in part to the greater variability in cell attachment to glass (coefficient of variation, 32.3% for glass compared with 10.0% for polystyrene). Employing polystyrene dishes, a novel microfouling assay was developed, based on the extraction and fluorometric determination of DNA. The assay was rapid, enabled the detection of as little as 0.15 mug of DNA per dish ( approximately 5,000 cells per mm), and showed good agreement with the direct count assay. The DNA method resulted in less variability among three replicates (average coefficient of variation, 7.06%) and allowed for estimation of bacterial density over a larger surface area per sample (1.89 x 10 mm) than was feasible with epifluorescence microscopy (0.06 to 0.1 mm).

The emergence and fate of horizontally acquired genes in Escherichia coli

Bacterial species, and even strains within species, can vary greatly in their gene contents and metabolic capabilities. We examine the evolution of this diversity by assessing the distribution and ancestry of each gene in 13 sequenced isolates of Escherichia coli and Shigella. We focus on the emergence and demise of two specific classes of genes, ORFans (genes with no homologs in present databases) and HOPs (genes with distant homologs), since these genes, in contrast to most conserved ancestral sequences, are known to be a major source of the novel features in each strain. We find that the rates of gain and loss of these genes vary greatly among strains as well as through time, and that ORFans and HOPs show very different behavior with respect to their emergence and demise. Although HOPs, which mostly represent gene acquisitions from other bacteria, originate more frequently, ORFans are much more likely to persist. This difference suggests that many adaptive traits are conferred by completely novel genes that do not originate in other bacterial genomes. With respect to the demise of these acquired genes, we find that strains of Shigella lose genes, both by disruption events and by complete removal, at accelerated rates.

Evaluation of the Hybrid Capture 2 CT/GC DNA tests and the GenProbe PACE 2 tests from the same male urethral swab specimens

BACKGROUND

A previous study demonstrated that Digene's Hybrid Capture 2 (HC2) DNA tests for detection of and (CT/GC) could be performed using cervical swab specimens collected in GenProbe transport media with significantly greater sensitivity for the detection of than with the GenProbe PACE 2 system.

GOAL

The goal was to assess the performance of HC2 tests in comparison with GenProbe PACE 2 tests for the detection of CT/GC in male urethral swab specimens.

STUDY DESIGN

A total of 1,202 male urethral swab specimens were collected in GenProbe PACE transport medium. All specimens were first tested with the PACE 2 system, followed by masked HC2 CT/GC testing. The GenProbe AMPLIFIED CT Assay (AMP CT) and PCR/SHARP Signal System (SHARP) were used for adjudication of discrepant results.

RESULTS

The prevalence rates for this population were 8.4% for and 14.6% for, based on the adjudicated results. The relative sensitivity and specificity for the detection of were 97.0% and 99.8% for HC2 and 69.3% and 98.3% for PACE 2, respectively. The relative sensitivities for the detection of were 98.9% for HC2 and 99.4% for PACE 2, with the same specificity of 99.9% for both tests. Agreement between the two testing methods was 95.4% for and 99.6% for.

CONCLUSION

The HC2 test is compatible with the GenProbe collection medium, with significantly greater sensitivity than the GenProbe PACE 2 test for detecting and similar sensitivities for detecting.

Recent developments in the molecular biology of anaplasmosis

Recent applications of DNA analysis, cloning, sequencing and expression technology have resulted in significant advances in our understanding of the hemoparasite Anaplasma marginale. Analysis of 16S ribosomal RNA has confirmed a phylogenetic position close to Ehrlichia sp. and Cowdria ruminantium. Intact genomic DNA of A. marginale digested with SfiI separates into bands from 14 to 170 kbp on pulse-field gels, with a total genome size of 1200-1260 kbp and G + C content of 56 mol%. Major surface proteins (MSP1-MSP5) have been identified and DNA coding sequences are available for most of these. These data have revealed that MSPs may be quite polymorphic between different geographic isolates, may be encoded by multi-gene families, and have some similar features to other prokaryotes including signal peptidase cleavage sites and gene regulatory sequences. Homologies have been detected between MSPs and immunodominant proteins of Cowdria ruminantium. Several MSPs have been expressed to high level and purified from recombinant Escherichia coli. MSP 1, 2 and 4 have potential for the development of vaccines and MSP3 and 5 for improved diagnostic assays.

Restriction fragment length polymorphism (RFLP) of genomic DNA of Moraxella (Branhamella) catarrhalis isolates in a hospital

Epidemiological typing, based on restriction fragment length polymorphism (RFLP) by pulsed-field gel electrophoresis (PFGE), was attempted for the 38 clinical isolates of Moraxella catarrhalis obtained at Shinshu University Hospital during the years 1987 and 1993. Digestion with SmaI or NotI generated well separable, 12 to 5 genomic DNA fragments ranging from 1,000 kb to 30 kb and the strains could be classified into 14 or 13 types, respectively. The electrophoretic profile differed with the strain in most of them and was hence useful to distinguish the each strain. Investigation for their RFLP have, however, suggested that majority of them, including the type strain ATCC25238, may have derived from a common ancestor.

Determination of genome sizes of Rickettsia spp. within the spotted fever group, using pulsed-field gel electrophoresis

The chromosome lengths of six spotted fever group Rickettsia species (Rickettsia rickettsii, R. conorii, R. rhipicephali, R. sibirica, R. australis, and R. akari) were estimated by pulsed-field gel electrophoresis. The genome size of R. rickettsii was about 2,100 kb, but the chromosome lengths of the five other species were, surprisingly, much lower and ranged between 1,200 and 1,300 kb.

Construction of physical and genetic maps of Chlamydia trachomatis serovar L2 by pulsed-field gel electrophoresis

We constructed the physical map of Chlamydia trachomatis serovar L2 by using three restriction endonucleases, NotI (GC[GGCCGC), SgrAI (C(A/G)[CCGG(T/G)G), and Sse8387I (CCTGCA[GG), and we analyzed the fragments by pulsed-field gel electrophoresis. A total of 25 restriction endonuclease sites and 13 genes and/or operons were located on the map. The genome size was determined to be 1,045 kb. Neither highly transcribed chlamydia genes nor developmental cycle-specific genes were clustered on the genome.

Physical map of the chromosome of Neisseria gonorrhoeae FA1090 with locations of genetic markers, including opa and pil genes

A physical map of the chromosome of Neisseria gonorrhoeae FA1090 has been constructed. Digestion of strain FA1090 DNA with NheI, SpeI, BglII, or PacI resulted in a limited number of fragments that were resolved by contour-clamped homogeneous electric field electrophoresis. The estimated genome size was 2,219 kb. To construct the map, probes corresponding to single-copy chromosomal sequences were used in Southern blots of digested DNA separated on pulsed-field gels, to determine how the fragments from different digests overlapped. Some of the probes represented identified gonococcal genes, whereas others were anonymous cloned fragments of strain FA1090 DNA. By using this approach, a macrorestriction map of the strain FA1090 chromosome was assembled, and the locations of various genetic markers on the map were determined. Once the map was completed, the repeated gene families encoding Opa and pilin proteins were mapped. The 11 opa loci of strain FA1090 were distributed over approximately 60% of the chromosome. The pil loci were more clustered and were located in two regions separated by approximately one-fourth of the chromosome.

Branhamella catarrhalis: an organism gaining respect as a pathogen

Branhamella catarrhalis was formerly regarded as a common, essentially harmless inhabitant of the pharynx. This misapprehension was caused, in part, by confusion with another pharyngeal resident, Neisseria cinerea. The two organisms can now be differentiated by the positive reactions of B. catarrhalis in tests for nitrate reduction and hydrolysis of tributyrin and DNase. B. catarrhalis is currently recognized as the third most frequent cause of acute otitis media and acute sinusitis in young children. It often causes acute exacerbations of chronic bronchopulmonary disease in older or immunocompromised adults and is incriminated occasionally in meningitis, endocarditis, bacteremia, conjunctivitis, keratitis, and urogenital infections. Virulence-associated factors, such as pili, capsules, outer membrane vesicles, iron acquisition proteins, histamine-synthesizing ability, resistance to the bactericidal action of normal human serum, and binding to the C1q complement component, have been identified in some strains. beta-Lactamase producing strains, first detected in 1976, have risen to approximately 75% worldwide. Thus far, however, practically all American strains of B. catarrhalis remain susceptible to alternative antibiotics. A possible selective advantage of recent isolates is their reportedly heightened tendency for adherence to oropharyngeal cells from patients with chronic bronchopulmonary disease.

Diversity of the Chlamydia trachomatis common plasmid in biovars with different pathogenicity

The 7.5-kb plasmid of Chlamydia trachomatis (CT) is believed to encode essential genes and might have a role in CT pathogenicity. Accordingly, analysis of plasmid-linked mutations in isolates from biovars with different pathogenic properties should help in identifying which plasmid-encoded genes, if any, may be involved in modulating virulence. For this purpose, the plasmid present in a low-virulence isolate (trachoma biovar, serotype D) was cloned and sequenced. Nucleotide changes were experimentally checked against the sequence of the plasmid variant from the highly virulent strain L2/434/Bu (LGV biovar). By aligning our data with two published sequences of different trachoma and LGV variants a general consensus structure was determined, comprising eight major open reading frames (ORF) and a number of points where there is consensus only between isolates of the same biovar (biovar-specific mutations). The degree of variation between different isolates is less than 1%. In particular, comparison of serotype-D and -L2 plasmids shows mutations which are generally silent or lead to few (one to four), often conservative, amino acid changes in ORFs 1, 2, 4, 5, 6, and 7. The protein encoded by ORF8 is completely conserved. In contrast, the polypeptide variants encoded by ORF3 show nine amino acid changes, seven of which are due to biovar-specific mutations.

Pulsed-field gel electrophoresis determination of the genome size of obligate intracellular bacteria belonging to the genera Chlamydia, Rickettsiella, and Porochlamydia

The chromosome length of obligate intracellular procaryotes was determined by pulsed-field gel electrophoresis of intact or NotI- and SfiI-restricted genomes. Sizes averaged 2,100, 1,720, 1,550, 2,650, and 1,450 kilobases for Rickettsiella grylli, Rickettsiella melolonthae, Porochlamydia buthi, Porochlamydia chironomi, and Chlamydia psittaci and Chlamydia trachomatis, respectively. An SfiI restriction map of the R. melolonthae genome was derived.

Laboratory diagnosis of human chlamydial infections

Chlamydia trachomatis is a human pathogen that causes ocular disease (trachoma and inclusion conjunctivitis), genital disease (cervicitis, urethritis, salpingitis, and lymphogranuloma venereum), and respiratory disease (infant pneumonitis). Respiratory chlamydioses also occur with infection by avian strains of C. psittaci or infection by the newly described TWAR agent. Diagnosis of most acute C. trachomatis infections relies on detection of the infecting agent by cell culture, fluorescent antibody, immunoassay, cytopathologic, or nucleic acid hybridization methods. Individual non-culture tests for C. trachomatis are less sensitive and specific than the best chlamydial cell culture system but offer the advantages of reduced technology and simple transport of clinical specimens. Currently available nonculture tests for C. trachomatis perform adequately as screening tests in populations in which the prevalence of infection is greater than 10%. A negative culture or nonculture test for C. trachomatis does not, however, exclude infection. The predictive value of a positive nonculture test may be unsatisfactory when populations of low infection prevalence are tested. Tests that detect antibody responses to chlamydial infection have limited utility in diagnosis of acute chlamydial infection because of the high prevalence of persistent antibody in healthy adults and the cross-reactivity due to infection by the highly prevalent C. trachomatis and TWAR agents. Assays for changes in antibody titer to the chlamydial genus antigen are used for the diagnosis of respiratory chlamydioses. A single serum sample that is negative for chlamydial antibody excludes the diagnosis of lymphogranuloma venereum.

Detection and quantitation of Anaplasma marginale in carrier cattle by using a nucleic acid probe

Cattle which have recovered from acute infection with Anaplasma marginale, a rickettsial hemoparasite of cattle, frequently remain persistently infected with a low-level parasitemia and serve as reservoirs for disease transmission. To fully understand the role of these carriers in disease prevalence and transmission, it is essential that low levels of parasitemia can be accurately detected and quantitated. We have developed a nucleic acid probe, derived from a portion of a gene encoding a 105,000-molecular-weight surface protein, that can detect A. marginale-infected erythrocytes. The probe is specific for A. marginale and can detect 0.01 ng of genomic DNA and 500 to 1,000 infected erythrocytes in 0.5 ml of blood, which is equivalent to a parasitemia of 0.000025%. This makes the probe at least 4,000 times more sensitive than light microscopy. Hybridization of the probe with treated blood from animals proven to be carriers of anaplasmosis showed that parasitemia levels were highly variable among carriers, ranging from greater than 0.0025 to less than 0.000025%. Parasitemia levels of individual animals on different dates were also variable. These results imply that, at any given time, individuals within a group of cattle may differ significantly in their abilities to transmit disease.

Analysis of the entire nucleotide sequence of the cryptic plasmid of Chlamydia trachomatis serovar L1. Evidence for involvement in DNA replication

Chlamydia trachomatis serovar L1/440/LN possesses a 7498bp plasmid which was designated pLGV440. The plasmid was cloned at the BamH1 site of pAT153 into Escherichia coli and the recombinant plasmid was designated pCTL1. A detailed restriction endonuclease map of pCTL1 was constructed. A fragment of the chlamydial plasmid was shown to function as a promoter in E. coli when placed upstream of the lacZ gene. The entire plasmid was sequenced by the chain termination method. Open reading frames were identified from the resulting consensus sequence together with a candidate for the plasmid origin of replication consisting of four perfect tandem repeats of a 22bp sequence, an A:T rich sequence and an open reading frame which could generate a 34.8kdal product. The predicted polypeptide products of the open reading frames were compared by computer with all reported protein sequences. Homology of the predicted polypeptide product of an open reading frame to the E. coli dnaB protein and the analogous product of gene 12 of bacteriophage P22 is described.

Recombination among protein II genes of Neisseria gonorrhoeae generates new coding sequences and increases structural variability in the protein II family

Expression of Neisseria gonorrhoeae Protein II (P.II) is subject to phase variation and antigenic variation. The P.II proteins made by one strain possess both unique and conserved antigenic determinants. To study the mechanism of antigenic variation, we cloned several P.II genes, using as probes a panel of monoclonal antibodies (MAbs) specific for unique determinants. The DNA sequences of three P.II genes showed that they shared a conserved framework, with two short hypervariable (HV) regions being responsible for most of the differences among them. We demonstrated that unique epitopes recognized by the MAbs were at least partially encoded by one of the HV regions. Moreover, we found that reassortment of the two HV regions among P.II genes occurs, generating increased structural and antigenic variability in the P.II protein family.

Characterization and sequence of a plasmid from the trachoma biovar of Chlamydia trachomatis

The 7.5-kb plasmid of Chlamydia trachomatis, trachoma biovar, was mapped for restriction enzyme sites and sequenced. The complete nucleotide sequence, the first reported for any chlamydial plasmid, revealed nine open reading frames which could code for polypeptides greater than 10 kDa. These putative polypeptides contain 35-47% hydrophobic amino acid residues. Two putative polypeptides of 30 kDa are highly basic and one of 23 kDa is acidic. A region composed of four 22-bp repeats, AT-rich clusters, an inverted repeat, and a 30-kDa basic protein is similar in organization to the origins of replication in a number of Escherichia coli plasmids. Northern blot analysis of the plasmid RNA showed transcripts longer than the length of the plasmid, suggesting a single transcription initiation signal.

Characterization of the new Chlamydia agent, TWAR, as a unique organism by restriction endonuclease analysis and DNA-DNA hybridization

Several molecular techniques were used for comparison of the novel Chlamydia agent, TWAR, with Chlamydia trachomatis and Chlamydia psittaci. Unlike all serotypes of C. trachomatis and most strains of C. psittaci, the eight TWAR isolates examined did not contain extrachromosomal DNA. TWAR was readily distinguished from C. trachomatis or C. psittaci by restriction endonuclease analysis, whereas identical or nearly identical restriction patterns were observed among the TWAR isolates. Southern blot analysis with a gene encoding a portion of the C. trachomatis serovar L2 major outer membrane protein as the probe showed that TWAR, like C. psittaci, contained sequences homologous to this gene. However, while the hybridization patterns were identical for all TWAR isolates, they differed from those of any of the other Chlamydia species tested. A PstI gene bank containing TWAR DNA was constructed in pUC19. Random fragments were purified and used for probing Chlamydia chromosomal digests. All of the five probes tested were TWAR specific, with the TWAR isolates showing identical patterns of homology. Qualitative studies of the DNA homology revealed that TWAR did not have significant homology to any of the Chlamydia strains assayed. Collectively, these results demonstrate that the TWAR isolates represent a single strain or closely allied genotypes and are clearly distinct from any of the other chlamydiae tested.

Restriction endonucleases for pulsed field mapping of bacterial genomes

Fundamental to many bacterial genome mapping strategies currently under development is the need to cleave the genome into a few large DNA fragments that can be resolved by pulsed field gel electrophoresis. Identification of endonucleases that infrequently cut a genome is of key importance in this process. We show that the tetranucleotide CTAG is extremely rare in most bacterial genomes with G+C contents above 45%. As a consequence, most of the sixteen bacterial genomes we have tested are cleaved less than once every 100,000 base pairs by one or more endonucleases that have CTAG in their recognition sequences: Xba I (TCTAGA), Spe I (ACTAGT), Avr II (CCTAGG) and Nhe I (GCTAGC). Similarly, CCG and CGG are the rarest trinucleotides in many genomes with G+C content of less than 45%. Thus, Sma I (CCCGGG), Rsr II (CGGWCCG), Nae I (GCCGGC) and Sac II (CCGCGG) are often suitable endonucleases for producing fragments that average over 100,000 base pairs from such genomes. Pulsed field gel electrophoresis of the fragments that result from cleavage with endonucleases that cleave only a few times per genome should assist in the physical mapping of many prokaryotic genomes.

Structural analysis of the pilE region of Neisseria gonorrhoeae P9

We have determined the nucleotide sequence of an expressed structural pilus gene (pilE) derived from Neisseria gonorrhoeae strain P9-2. Detailed analysis of nucleotide sequences upstream from pilE revealed a silent, truncated pilin gene segment that was linked to families of DNA elements (RS1 and RS3) that have previously been identified at the major silent pilin gene locus (pilS1) and at pilE of the independently isolated N. gonorrhoeae strain MS11ms. A nucleotide sequence downstream from pilE was reminiscent of the recognition sequences of several recombinases, including Tn3 tnpR product (resolvase), suggesting a possible role for site-specific events in the recombinational modulation of pilus expression.

A common plasmid of Chlamydia trachomatis

A 7.4-kb plasmid is a common and perhaps essential component of the Chlamydia trachomatis genome. This plasmid occurs as 10 copies per chlamydial chromosomal equivalent. It is unable to replicate in Escherichia coli. Complete plasmid genomes from eight serovars of C. trachomatis have been isolated in E. coli as cloned sequences ligated to pBR322. Restriction enzyme cleavage site mapping indicates that these plasmids are closely related. Homologous plasmid sequences have also been detected by DNA hybridization in all of the 200 clinically isolated strains of C. trachomatis which have been examined. DNA sequences homologous to the C. trachomatis plasmid were not found in eucaryotic DNA nor in a plasmid of similar size isolated from C. psittaci. C. trachomatis plasmid genes are expressed in vivo and the plasmid encoded gene products may play a role in the intracellular growth of this organism. Plasmid encoded genes were also expressed from the cloned C. trachomatis plasmid in E. coli minicells and using an E. coli S-30 in vitro transcription translation extract.

Comparison of Chlamydia psittaci isolates by DNA restriction endonuclease analysis

Preparations of DNA from 12 Chlamydia psittaci isolates and one Chlamydia trachomatis strain were compared by restriction endonuclease analysis. Polyacrylamide gel electrophoresis, followed by silver staining, resulted in optimal resolution of fragments generated by digestion. By this technique, four distinct electropherotypes were demonstrated when ovine abortion, ovine arthritis, and avian and Cal10 strains of C. psittaci were examined. Minor profile differences allowed the discrimination of avian isolates derived from psittacine and columbiforme species, and the Cal10 DNA electropherotype was shown to have features in common with these profiles. However, there were no detectable differences in the DNA patterns of eight ovine abortion isolates.

Characterization of Chlamydia DNA by restriction endonuclease cleavage

The DNA from six serovars of Chlamydia trachomatis, lymphogranuloma venereum (LGV) I, LGV II, LGV III, B, C, and D, and from Chlamydia psittaci was extracted, treated with restriction endonuclease enzymes, and run on agarose gels. By using this technique, the DNA of C. trachomatis could be clearly differentiated from C. psittaci DNA. A comparison of the DNA from the different serovars of C. trachomatis revealed similar patterns with and without detectable differences. LGV I, LGV II, LGV III, B, and C revealed no differences when treated with BamHI, HaeIII, XbaI, and XhoI. LGV III DNA, when cleaved with EcoRI and HhaI, had a major band migrating faster than the other two LGV serovars. Serovar D had a different pattern from all other strains tested when cleaved with BamHI, EcoRI, HhaI, HincI, and XhoI. When treated with SacI and HgaI, LGV II displayed a unique band not seen in the other LGV serovars. Differences in strains could be attributed to both chromosomal and plasmid DNA.

Chlamydia trachomatis has penicillin-binding proteins but not detectable muramic acid

Chlamydia trachomatis LGV-434 was grown in HeLa 229 cells. Benzylpenicillin completely inhibited the formation of infectious elementary bodies (EBs) at a concentration of 19 pmol/ml or higher and produced abnormally large reticulate bodies (RBs) in the inclusions at 30 pmol/ml or higher. The possible targets for penicillin in C. trachomatis were three penicillin-binding proteins (PBPs) which were identified in the Sarkosyl-soluble fractions of both RBs and EBs. The apparent subunit molecular weights were 88,000 (PBP 1), 61,000 (BPB 2), and 36,000 (PBP 3). The 50% binding concentrations of [3H]penicillin for PBPs 1 to 3 in EBs and RBs were between 7 and 70 pmol/ml. Such high susceptibility to penicillin was shown by an organism that did not have detectable muramic acid (less than 0.02% by weight) in preparations of either whole cells or sodium dodecyl sulfate-insoluble residues.

Between history and physics

Biology has traditionally occupied a middle ground between the determinism of classical physics and the uncertainties of history. These issues are analyzed with respect to statistical laws which are applied to the prebiotic domain and strategy laws which characterize evolutionary biology. The differences in approach between biology and physics are discussed in detail. The origin of life is discussed in the context of physical chemical laws. A scenario for biogenesis is presented in terms of known molecular hardware. Evolutionary biology is then examined with respect to the kinds of laws that are possible in a domain where thermal fluctuations (mutations) have macroscopic effects. Game theory is employed to demonstrate the kinds of theory appropriate to this historical domain. The transition point between physics and history is the origin and development of the code. This is discussed and it is concluded that we are not yet able to assign the code to either the deterministic domain or to the arena of history.

The relation of basic biology to pathogenic potential in the genus Chlamydia

Chlamydiae are obligately intracellular procaryotic parasites, and their activities as agents of human disease are determined to a large degree by their intracellular way of life. The inside of a host cell is a hostile environment, and few microorganisms survive and multiply intracellularly. Those that do have evolved adaptations that fit them for life inside other cells. Apart from the viruses, chlamydiae are the infectious agents most highly adapted to intracellular life. Of all the properties of chlamydiae, the ones most likely to determine their pathogenic potential are those that reflect their adaptations to life inside host cells. Wherever possible, these chlamydial activities will be indentified and described.

Purification and partial characterization of the major outer membrane protein of Chlamydia trachomatis

Elementary bodies (EB) of Chlamydia trachomatis serotypes C, E, and L2 were extrinsically radioiodinated, and whole-cell lysates of these serotypes were compared by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Autoradiography of the polypeptide profiles identified a major surface protein with an apparent subunit molecular weight of 39,500 that was common to each C. trachomatis serotype. The abilities of nonionic (Triton X-100), dipolar ionic (Zwittergent TM-314), mild (sodium deoxycholate and sodium N-lauroyl sarcosine), and strongly anionic (SDS) detergents to extract this protein from intact EB of the L2 serotype were investigated by SDS-PAGE analysis of the soluble and insoluble fractions obtained after each detergent treatment. Only SDS readily extracted this protein from intact EB. Sarkosyl treatment selectively solubilized the majority of other EB proteins, leaving the 39,500-dalton protein associated with the Sarkosyl-insoluble fraction. Ultrastructural studies of the Sarkosyl-insoluble EB pellet showed it to consist of empty EB particles possessing an apparently intact outer membrane. No structural evidence for a peptidoglycan-like cell wall was found. Morphologically these chlamydial outer membrane complexes (COMC) resembled intact chlamydial EB outer membranes. The 39,500-dalton outer membrane protein was quantitatively extracted from COMC by treating them with 2% SDS at 60 degrees C. This protein accounted for 61% of the total COMC-associated protein, and its extraction resulted in a concomitant loss of the COMC membrane structure and morphology. The soluble extract obtained from SDS-treated COMC was adsorbed to a hydroxylapatite column and eluted with a linear sodium phosphate gradient. The 39,500-dalton protein was eluted from the column as a single peak at a phosphate concentration of approximately 0.3 M. The eluted protein was nearly homogeneous by SDS-PAGE and appeared free of contaminating carbohydrate, glycolipid, and nucleic acid. Hyperimmune mouse antiserum prepared against the 39,500-dalton protein from serotype L2 reacted with C. trachomatis serotypes Ba, E, D, K, L1, L2, and L3 by indirect immunofluorescence with EB but failed to react with serotypes A, B, C, F, G, H, I, and J, with the C. trachomatis mouse pneumonitis strain, or with the C. psittaci feline pneumonitis, guinea pig inclusion conjunctivitis, or 6BC strains. Thus, the 39,500-dalton major outer membrane protein is a serogroup antigen of C. trachomatis organisms.

Persistent infection of mouse fibroblasts (L cells) with Chlamydia psittaci: evidence for a cryptic chlamydial form

When monolayers of mouse fibroblasts (L cells) were infected with enough Chlamydia psittaci (strain 6BC) to destroy most of the host cells, 1 in every 10(5) to 10(6) originally infected cells gave rise to a colony of L cells persistently infected with strain 6BC. In these populations, the density of L cells and 6BC fluctuated periodically and reciprocally as periods of host cell increase were followed by periods of parasite multiplication. Successive cycles of L-cell and 6BC reproduction were sustained indefinitely by periodic transfer to fresh medium. Isolation of L cells and 6BC from persistent infections provided no evidence that there had been any selection of variants better suited for coexistence. Persistently infected populations consisting mainly of inclusion-free L cells yielded only persistently infected clones, grew more slowly, and cloned less efficiently. They were also almost completely resistant to superinfection with high multiplicities of either 6BC or the lymphogranuloma venereum strain 440L of Chlamydia trachomatis. These properties of persistently infected L cells may be accounted for by assuming that all of the individuals in these populations are cryptically infected with 6BC and that cryptic infection slows the growth of the host cell and makes it immune to infection with exogenous chlamydiae. According to this hypothesis, the fluctuations in host and parasite density occur because some factor periodically sets off the conversion of cryptic chlamydial forms into reticulate bodies that multiply and differentiate into infectious elementary bodies in a conventional chlamydial developmental cycle.

Genome size of the rickettsia Coxiella burnetii

The genome size of Coxiella burnetii Nine Mile strain was determined by the method of initial rate of deoxyribonucleic acid renaturation. The mean value obtained was 1.04 X 10(9) daltons.

The biology of the gonococcus

Gonorrhea has been known since antiquity. Today, this disease is the most commonly reported infectious disease in the U.S. The natural environment of the etiological agent, Neisseria gonorrhoeae, is man. In this host, the organism usually parasitizes mucosal surfaces populated by columnar epithelial cells. Under certain conditions, the gonococcus may disseminate or spread to adjacent organs. The gonococcus is well adapted to its environment and is a successful parasite. Until recently, gonococci were uniformly sensitive to penicilin. However, a plasmid encoding beta-lactamase has been identified in some isolates. Most strains exhibit specific requirements for various amino acids, vitamins, purines, and pyrimidines. Only glucose, pyruvate, and lactate are utilized as sources of energy. Glucose is dissimilated by a combination of the Entner-Doudoroff and pentose phosphate pathways. A tricarboxylic acid cycle is also present and active under certain conditions. Structurally, the cell envelope of the gonococcus resembles that of a typical Gram-negative bacterium. Gonococci are highly autolytic, especially in older cultures or after depletion of the energy source. Autolysis is not due solely to peptidoglycan hydrolysis, but appears to involve a destabilization of the outer membrane as well. Cell surface components such as pili, lipopolysaccharide, outer membrane proteins, and a capsule are associated with the virulence and pathogenicity of this organism.

The chlamydia: molecular biology of procaryotic obligate parasites of eucaryocytes

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Contribution of a TEM-1-like beta-lactamase to penicillin resistance in Neisseria gonorrhoeae

Two beta-lactamase-producing strains of Neisseria gonorrhoeae were studied. The substrate profile, molecular weight, and isoelectric point of their beta-lactamases were similar to those of the TEM-1 enzyme produced by many gram-negative bacilli. The gonococcal beta-lactamase was cell bound during exponential growth and was most likely located in the periplasm. Penicillin hydrolysis was efficient in intact cells, suggesting that the cell-bound beta-lactamase was freely accessible to benzylpenicillin. Both beta-lactamase-producing strains of N. gonorrhoeae contained an additional multicopy plasmid with a mass of 3.3 megadaltons (Mdal). A spontaneous penicillin-susceptible revertant lacked both beta-lactamase activity and the 3.3-Mdal plasmid, providing evidence for plasmid-mediated penicillin resistance. During a shift from GC medium to rich MOPS medium, growth of the penicillin-susceptible revertant in contrast to that of the plasmid-carrying strain was markedly impaired, suggesting a physiological effect due to the presence of the 3.3-Mdal plasmid.

Synthesis of ribonucleotides and their participation in ribonucleic acid synthesis by Coxiella burnetii

Synthesis of ribonucleic acid (RNA) by the deoxyribonucleic acid-dependent RNA polymerase of Coxiella burnetii required adenosine, uridine, guanosine, and cytidine 5'-triphosphates. Cell-free preparations of this obligate intracellular procaryotic parasite had competence to phosphorylate ribonucleoside mono- and diphosphates in the presence of exogenous adenosine and guanosine 5'-triphosphates to the corresponding di- and triphosphates. C. burnetii contained about 2 nmol of adenosine 5'-triphosphate per mg of protein, which could serve as a approximately P donor for in vivo synthesis of nucleoside triphosphates. The latter were then used as substrates in the synthesis of RNA in a coordinated metabolic system with C. burnetii RNA polymerase. It is suggested that during infection the rickettsiae might obtain the nucleotides necessary for RNA synthesis from the vacuoles in which C. burnetii proliferates.

Renaturation kinetics and thermal stability of DNA in aqueous solutions of formamide and urea

This paper reports the results of a systematic study of the effects of formamide and urea on the thermal stability and renaturation kinetics of DNA. Increasing concentrations of urea in the range 0 to 8 molar lower the Tm by 2.25 degrees C per molar, and decreases the renaturation rate by approximately 8 percent per molar. Increasing concentrations of formamide in the range from 0 to 50 percent lowers the Tm by 0.60 degrees C per percent formamide for sodium chloride concentrations ranging from 0.035M to 0.88M. At higher salt concentrations the dependence of Tm on percent formamide was found to be slightly greater. Increasing formamide concentration decreases the renaturation rate linearly by 1.1% per percent formamide such that the optimal rate in 50% formamide is 0.45 the optimal rate in an identical solution with no formamide. The effects of urea and formamide on the renaturation rates of DNA are explained by consideration of the viscosities of the solutions at the renaturation temperatures.

Proteins of typhus and spotted fever group rickettsiae

Purified radioactive rickettsiae were obtained from irradiated and cycloheximide-inhibited L cells, and their proteins were analyzed by polyacrylamide gel electrophoresis. Rickettsial species could be distinguished by comparing the relative mobilities of constituent proteins after migration of two differentially labeled preparations in a single gel. Distinct differences were observed in gel patterns of rickettsiae from the typhus and spotted fever groups, as well as with different species within a group. Rickettsial organisms causing murine and epidemic typhus were clearly distinguished, as were the causative agentsof boutonneuse fever and rickettsialpox. The use of both internal and external molecular weight standards allowed molecular weight estimates for 19 proteins from both Rickettsia prowazekii and Rickettsia conorii. A flexible system for designating rickettsial proteins is proposed that lends itself to modification as more detailed analysis progresses.

The so20,w of unsheared DNA from whole cell lysates of Escherichia coli

We present measurements of the sedimentation coefficients of DNA present in whole cell lysates of E. coli. The method used is a preparative version of the band sedimentation experiment of Bruner and Vinograd. We show that in order to obtain reliable data on the time dependence of sedimentation, it is necessary to accelerate and decelerate the rotor over much longer times than the standard centrifuge allows. We describe the necessary modifications to the preparative centrifuge and use them to determine the So20,W of unsheared E. coli DNA. The value for the fastest moving components in the lysate is 220 S. The molecular weight of the DNA corresponding to this sedimentation coefficient is probably 1.7 X 10(9) g/mole. However, alternative values cannot be ruled out.

Chromosomal location of antibiotic resistance genes in Neisseria gonorrhoeae

Transformation with purified plasmid and chromosomal deoxyribonucleic acid from a clinical isolate of Neisseria gonorrhoeae showed that each of seven loci affecting drug resistance (penA, penB, ery, str, tet, chl, and env) was chromosomal.

Isolation of intracellular symbiotes by immune lysis of flagellate protozoa and characterization of their DNA

A new method dependent on immune lysis is described for the isolation of intracellular symbiotes from two species of flagellate protozoa Blastocrithidia culicis and Crithidia oncopelti. The symbiote-containing flagellates are exposed to complement and antisera prepared in rabbits against symbiote-free organisms. The immune lysis seems to weaken the plasma membranes of the flagellates so that subsequent application of gentle shearing force liberates the intracellular entities in an undamaged condition. The symbiotes are then separated from other cellular components by DNAse digestion and differential centrifugation. The average recovery of symbiotes isolated by this method is 20%. Light and electron microscopy establishes the structural integrity and numerical abundance of isolated symbiotes in the final fractions. Integrity of symbiotes is further indicated by the high activity of a marker enzyme, uroporphyrinogen I synthetase. The DNA's of symbiote-containing and symbiote-free flagellates, and of isolated symbiotes were purified and compared after isopycnic centrifugation. The comparison establishes the presence of DNA's in symbiotes of both species. The guanine-cytosine (G-C) content of symbiote DNA differs from that of host DNA's in C. oncopelti, but resembles that of kinetoplast DNA in B. culicis. The latter observation was further shown by heat denaturation study. Renaturation kinetics indicate that the genome complexity of symbiote DNA in B. culicis is similar to that of bacteria.