Biosynthesis and secretion of recombinant human growth hormone in Pichia pastoris

Mature human growth hormone (hGH) cDNA was cloned by homologous recombination into the yeast Pichia pastoris genome. The hGH gene expression was placed under the control of the methanol-inducible alcohol oxidase 1 (AOX1) gene promoter and the Saccharomyces cerevisiae -factor signal sequence to direct the secretion of recombinant human growth hormone (rhGH) into the growth medium. O₂-limited induction of recombinant yeast strains in shake tubes with 3 ml of culture medium produced up to 11 mg rhGH l^–1, while high cell density cultures using a 2-l bioreactor produced about 49 mg rhGH l^–1 achieving 40% of total protein of the culture medium supernatant.     

Human growth hormone expressed in tobacco cells as an arabinogalactan-protein fusion glycoprotein has a prolonged serum life

Therapeutic proteins with molecular weights lower than 40 kDa often have short serum half-lives due to their susceptibility to serum proteases and rapid renal clearance. Chemical derivatization, such as PEGylation, or expression as serum albumin fusions increases molecular mass and overcome these problems but at the expense of decreased bioactivity. Here we applied a new method that yields biologically potent recombinant human growth hormone (rhGH) with increased serum half-life when expressed as an arabinogalactan-protein (AGP) in tobacco BY-2 cells. Thus, rhGH was expressed with 10 repeats of the AGP glycomodule Ser-Hyp (SO) at the C-terminus (rhGH-(SO)₁₀). We also expressed rhGH as an AGP-enhanced green fluorescent protein (EGFP) fusion, designated rhGH-(SO)₁₀-EGFP, to assess the cellular distribution of the glycoprotein, which was mainly extracellular. Recombinant hGH-(SO)₁₀ bound the hGH receptor with an affinity similar to that of a rhGH standard, stimulated the same intracellular signaling pathway as hGH, but possessed an in vivo serum half-life more than sixfold that of the hGH control. Furthermore, rhGH-(SO)₁₀ gave a 500 fold greater secreted yield than the non-glycosylated control rhGH that was also targeted for secretion. Detailed analysis of the rhGH-(SO)₁₀ glycans indicated a conserved structure with relatively little microheterogeneity and an average size of 25 monosaccharide residues. These results were consistent with earlier work expressing interferon α2b as an AGP chimera and further demonstrate the feasibility of this approach to the production of long-acting, biologically potent therapeutic proteins by plant cells.     

Fluorescence‐based sensor for selective and sensitive detection of amoxicillin (Amox) in aqueous medium: Application to pharmaceutical and biomedical analysis

We here for the first time demonstrate an analytical approach for the highly selective and sensitive detection of amoxicillin (Amox) in aqueous medium based on the fluorescence quenching of quantum dots (QDs). The change in fluorescence intensity of mercaptopropionic acid‐capped cadmium sulphide (MPA‐CdS) QDs is attributed to the increasing concentration of Amox. The results show that the fluorescence quenching of QDs by Amox takes place through both static and dynamic types of quenching mechanism. The fluorescence quenching of QDs with increase in concentration of Amox shows the linear range between 5 μg ml^?1 and 30 μg ml^?1 and the limit of detection (LOD) is 5.19 μg ml^?1. There is no interference of excipients, which are commonly present in pharmaceutical formulation and urine samples. For the practical application approach, the developed method has been successfully applied for the determination of Amox in pharmaceutical formulations and urine samples with acceptable results.     

Expression system for synthesis and purification of recombinant human growth hormone in Pichia pastoris and structural analysis by MALDI-ToF Mass Spectrometry

An expression system in Pichia pastoris for the production and purification of recombinant human growth hormone (rHGH) was designed and implemented. hGH cDNA sequence was cloned into pPICZalphaA vector under the control of AOX1 promoter, which included a polyhistidine-tag on the amino terminal end to enable affinity purification and a target site for Factor Xa protease such that protease cleavage in vitro would produce rhGH without any non-native N- and C-termini. Analyses of the affinity-purified rhGH product by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) showed a spectral peak at m/z 23699. Purified product digested with Factor Xa protease had a molecular mass of 22132 kDa. The molecular mass difference before and after Factor Xa protease digestion expectedly corresponds to the 12 amino acids in the rhGH amino terminus, which includes the EcoRI digestion site (Glu-Phe), the 6xHis tag for affinity purification, and the Factor Xa protease recognition sequence (Ile-Glu-Gly-Arg), a result that also indicates that the signal peptide was properly processed by P. pastoris. N-Terminal sequence analysis of the Factor Xa protease trimmed recombinant product confirmed the mature hGH sequence. Thus, the system designed functioned with its intended purpose effectively in expression, cleavage, and purification of the recombinant product.     

Quantitative Detection of Escherichia coli O157 in Surface Waters by Using Immunomagnetic Electrochemiluminescence

A protocol for the quantitative detection of Escherichia coli O157 in raw and concentrated surface waters using immunomagnetic electrochemiluminescence (IM-ECL) was developed and optimized. Three antibody sandwich formats were tested: commercial anti-O157:H7 IM beads, IM beads made in-house with a polyclonal anti-O157:H7 immunoglobulin G (IgG), or IM beads made in-house with a monoclonal anti-O157:H7 IgG coupled with a polyclonal anti-O157:H7 IgG to which an electrochemiluminescent label (TAG) was attached. The monoclonal IM bead-polyclonal TAG format was chosen for optimization because it gave lower background levels and linear regression slopes of ca. 1.0, indicative of a constant ECL signal per cell. The dynamic range was ca. 10¹ to 10⁵ cells ml⁻¹ in phosphate-buffered saline and in raw water samples. The monoclonal IM beads selectively captured E. coli O157 cells in the presence of ca. 10⁸ cells of a non-O157 strain of E. coli ml⁻¹. Background ECL signals from concentrated (100-fold) water samples were substantially higher and more variable than raw water samples. The background signal was partially eliminated by the addition of polyvinylpolypyrrolidone. Successive cell capture incubations, termed sequential bead capture (SBC), were optimized for establishing baseline ECL values for individual water samples. The linear dynamic range with SBC was ca. 10² to 10⁵ E. coli O157 cells ml of concentrated water⁻¹. To validate the protocol, 10-liter surface water samples were spiked with ca. 5,000 E. coli O157 (Odwalla) cells and concentrated by vortex filtration, and 1- or 3-ml aliquots were analyzed by IM-ECL. Differential ECL signals (SBC) from 1- and 3-ml samples were statistically significant and were generally consistent with standard curves for these cell concentrations. Enrichments were conducted with aliquots of spiked raw water and concentrated water using EC broth and minimal lactose broth (MLB). All tubes with concentrated water became turbid and gave a positive ECL response for E. coli O157 (>10,000 ECL units); MLB gave a somewhat higher detection rate with spiked raw water. The potential sensitivity of the IM-ECL assay is ca. 25 E. coli O157 cells ml of raw water⁻¹, 25 cells 100 ml of 100-fold concentrated water⁻¹, or 1 to 2 viable cells liter⁻¹ with concentration and enrichment. The IM-ECL assay appears suitable for routine analysis and screening of water samples.     

Negative Regulation of Human Growth Hormone Gene Expression by Insulin Is Dependent on Hypoxia-inducible Factor Binding in Primary Non-tumor Pituitary Cells

Insulin controls growth hormone (GH) production at multiple levels, including via a direct effect on pituitary somatotrophs. There are no data, however, on the regulation of the intact human (h) GH gene (hGH1) by insulin in non-tumor pituitary cells, but the proximal promoter region (nucleotides −496/+1) responds negatively to insulin in transfected pituitary tumor cells. A DNA-protein interaction was also induced by insulin at nucleotides −308/−235. Here, we confirmed the presence of a hypoxia-inducible factor 1 (HIF-1) binding site within these sequences (−264/−259) and investigated whether HIF-1 is associated with insulin regulation of “endogenous” hGH1. In the absence of primary human pituitary cells, transgenic mice expressing the intact hGH locus in a somatotroph-specific manner were generated. A significant and dose-dependent decrease in hGH and mouse GH RNA levels was detected in primary pituitary cell cultures from these mice with insulin treatment. Increasing HIF-1α availability with a hypoxia mimetic significantly decreased hGH RNA levels and was accompanied by recruitment of HIF-1α to the hGH1 promoter in situ as seen with insulin. Both inhibition of HIF-1 DNA binding by echinomycin and RNA interference of HIF-1α synthesis blunted the negative effect of insulin on hGH1 but not mGH. The insulin response is also sensitive to histone deacetylase inhibition/trichostatin A and associated with a decrease in H3/H4 hyperacetylation in the proximal hGH1 promoter region. These data are consistent with HIF-1-dependent down-regulation of hGH1 by insulin via chromatin remodeling specifically in the proximal promoter region.     

Discrimination of Recombinant from Natural Human Growth Hormone Using DNA Aptamers

Detection of athletes who use synthetic human growth hormone (hGH; or somatotropin) to enhance physical strength and obtain an advantage in competitive sports is a formidable problem, as rhGH is virtually identical to the natural pituitary hormone. However, some post-translational and other modifications have been documented by chromatographic separation and mass spectrometry (MS) in a small percentage of rhGH. In the present work, development of DNA aptamers against research-grade rhGH and natural hGH with adsorption of the rhGH aptamers against natural hGH was shown to produce a small family of aptamer sequences that bound consistently with greater affinity to rhGH over a low nanogram-to-microgram range in ELISA-like microplate assays. This collection of rhGH discriminatory aptamer sequences shared some short sequence segments and secondary structural features. The top rhGH discriminatory aptamers also appeared to cross-react with human myoglobin and BSA but not with bone collagen peptides and an unrelated viral envelope peptide. The cross-reactivity results suggested several strings of up to five consecutive amino acids that might serve as common epitopes for aptamer binding. SDS-PAGE revealed that the rhGH existed largely as a 45-kDa dimer, and the natural hGH was almost exclusively monomeric. The existence of the rhGH dimer suggests that a discontinuous “bridge” epitope may exist on the rhGH, which spans the subunits, thereby accounting somewhat for the difference in detection. Overall, these results suggest that aptamers might be useful for routine, presumptive laboratory screening to identify athletes who are potentially cheating by administration of rhGH.     

Facile and sensitive detection of protamine by enhanced room-temperature phosphorescence of Mn-doped ZnS quantum dots

Quantum dot (QD) nanohybrids provide an effective route to explore the new properties of materials and are increasingly used as highly valuable sensitive (bio) chemical probes. Interestingly, the room-temperature phosphorescence (RTP) of 3-mercaptopropionic acid (MPA)-capped Mn-doped ZnS QDs could be remarkably enhanced by the addition of protamine. Based on the above finding, a simple, sensitive, and selective method for rapid detection of protamine was successfully designed. With this method, protamine as a cationic peptide interacts electrostatically with MPA-capped Mn-doped ZnS QDs to form MPA-capped Mn-doped ZnS QD/protamine complexes, which leads to the aggregation of QDs and enhances the RTP intensity. Under the optimized conditions, the RTP intensity change was linearly proportional to the concentration of protamine in the range 0.2–3.0 μg ml⁻¹, and the limit of detection was 0.14 μg ml⁻¹. The proposed method was successfully applied to detect protamine in protamine sulfate injection and human serum samples with satisfactory results, and the recovery ranged from 96.5 to 105.6%.     

Expression system for recombinant human growth hormone production from Bacillus subtilis

We demonstrate for the first time, an expression system mimicking serine alkaline protease synthesis and secretion, producing native form of human growth hormone (hGH) from Bacillus subtilis. A hybrid‐gene of two DNA fragments, i.e., signal (pre‐) DNA sequence of B. licheniformis serine alkaline protease gene (subC) and cDNA encoding hGH, were cloned into pMK4 and expressed under deg‐promoter in B. subtilis. Recombinant‐hGH (rhGH) produced by B. subtilis carrying pMK4::pre(subC)::hGH was secreted. N‐terminal sequence and mass spectrometry analyses of rhGH confirm the mature hGH sequence, and indicate that the signal peptide was properly processed by B. subtilis signal‐peptidase. The highest rhGH concentration was obtained at t = 32 h as C_rhGH = 70 mg L^?1 with a product yield on substrate Y_rhGH/S = 9 g kg^?1, in a glucose based defined medium. Fermentation characteristics and influence of hGH gene on the rhGH production were investigated by comparing B. subtilis carrying pMK4::pre(subC)::hGH with that of carrying merely pMK4. Excreted organic‐acid concentrations were higher by B. subtilis carrying pMK4::pre(subC)::hGH, whereas excreted amino‐acid concentrations were higher by B. subtilis carrying pMK4. The approach developed is expected to be applicable to the design of expression systems for heterologous protein production from Bacillus species. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Development of a quantum dot molecularly imprinted polymer sensor for fluorescence detection of atrazine

Atrazine is a common agricultural pesticide which has been reported to occur widely in surface drinking water, making it an environmental pollutant of concern. In the quest for developing sensitive detection methods for pesticides, the use of quantum dots (QDs) as sensitive fluorescence probes has gained momentum in recent years. QDs have attractive and unique optical properties whilst coupling of QDs to molecularly imprinted polymers (MIPs) has been shown to offer excellent selectivity. Thus, the development of QD@MIPs based fluorescence sensors could provide an alternative for monitoring herbicides like atrazine in water. In this work, highly fluorescent CdSeTe/ZnS QDs were fabricated using the conventional organometallic synthesis approach and were then encapsulated with MIPs. The CdSeTe/ZnS@MIP sensor was characterized and applied for selective detection of atrazine. The sensor showed a fast response time (5 min) upon interaction with atrazine and the fluorescence intensity was linearly quenched within the 2–20 mol L^?1 atrazine range. The detection limit of 0.80 × 10^?7 mol L^?1 is comparable to reported environmental levels. Lastly, the sensor was applied in real water samples and showed satisfactory recoveries (92–118%) in spiked samples, hence it is a promising candidate for use in water monitoring.     

Immunoquantitative Real-Time PCR for Detection and Quantification of Staphylococcus aureus Enterotoxin B in Foods

A real-time immunoquantitative PCR (iqPCR) method for detection of Staphylococcus aureus enterotoxin B (SEB) was developed and evaluated using both pure cultures and foods. The assay consisted of immunocapture of SEB and real-time PCR amplification of the DNA probe linked to the detection antibody. iqPCR was compared to an in-house enzyme-linked immunosorbent assay (ELISA) using the same couple of capture-detection antibodies and to commercial kits for detection of S. aureus enterotoxins (SE). The iqPCR was approximately 1,000 times more sensitive (<10 pg ml⁻¹) than the in-house ELISA and had a dynamic range of approximately 10 pg ml⁻¹ to approximately 30,000 pg ml⁻¹. iqPCR was not inhibited by any of the foods tested and was able to detect SEB present in these foods. No cross-reactivity with SE other than SEB was observed. Application of iqPCR for detection of SEB in cultures of S. aureus revealed the onset of SEB production after 4 h of incubation at 22, 37, and 42°C, which was in the first half of the exponential growth phase. The total amounts of SEB produced by the two strains tested were larger at 42°C than at 37°C and were strain dependent.     

Development of an In Vitro Bioassay for Clostridium botulinum Type B Neurotoxin in Foods That Is More Sensitive than the Mouse Bioassay

A novel, in vitro bioassay for detection of the botulinum type B neurotoxin in a range of media was developed. The assay is amplified by the enzymic activity of the neurotoxin’s light chain and includes the following three stages: first, a small, monoclonal antibody-based immunoaffinity column captures the toxin; second, a peptide substrate is cleaved by using the endopeptidase activity of the type B neurotoxin; and finally, a modified enzyme-linked immunoassay system detects the peptide cleavage products. The assay is highly specific for type B neurotoxin and is capable of detecting type B toxin at a concentration of 5 pg ml⁻¹ (0.5 mouse 50% lethal dose ml⁻¹) in approximately 5 h. The format of the test was found to be suitable for detecting botulinum type B toxin in a range of foodstuffs with a sensitivity that exceeds the sensitivity of the mouse assay. Using highly specific monoclonal antibodies as the capture phase, we found that the endopeptidase assay was capable of differentiating between the type B neurotoxins produced by proteolytic and nonproteolytic strains of Clostridium botulinum type B.     

Enzyme-Linked Immunosorbent Assays for the Specific and Sensitive Quantification of Methanosarcina mazei and Methanobacterium bryantii

Three microtitration plate enzyme-linked immunosorbent assays (ELISAs) have been developed: a competitive ELISA and a two-site (or indirect sandwich) ELISA for Methanosarcina mazei S6 and a two-site ELISA for Methanobacterium bryantii FR-2. The assays were sensitive, with limits of cell protein detection of 3 ng ml⁻¹, 5 ng ml⁻¹, and 50 ng ml⁻¹, respectively, and showed good precision. The M. mazei assays used monoclonal antibodies and were entirely species specific, showing no cross-reaction with methanogens of other genera or with other species of the same genus. The Methanobacterium bryantii assay, which used two polyclonal antisera, showed only a slight cross-reaction with one other Methanobacterium species but no cross-reaction with methanogens of other genera. The use of the ELISAs for quantitative analysis of mixed cultures and of sewage sludge samples was investigated. Sludge diluted at 1:10³ or more caused no significant interference in any of the three ELISAs. Various cultures of bacteria, methanogens, and nonmethanogens at a protein concentration of 50 μg ml⁻¹ showed no significant interference in the M. mazei competitive assay and the Methanobacterium bryantii two-site assay, although they did cause falsely low results in the M. mazei two-site assay.     

Characterization of recombinant human growth hormone variants from sodium hyaluronate-based sustained release formulation of rhGH under heat stress

This study provides the findings of investigations of potential product-related variants on recombinant human growth hormone (rhGH) in a once-weekly sustained release formulation (SR–rhGH) of sodium hyaluronate microparticles and on the rhGH bulk solution used as the active ingredient for SR–rhGH under extreme stress conditions of 24 h at 60 °C. The extent of rhGH degradation was much higher in solution (33%) than in SR–rhGH (10%). The degradation products, especially Met14 sulfoxide and deamidated rhGH variants, were separated and quantified by a modified reversed-phase high-performance liquid chromatography (RP–HPLC) method at reduced flow rate. The primary degradation product of rhGH was found to be deamidated rhGH, although an unknown peak was also detected. In contrast, the primary degradation product of SR–rhGH was Met14 sulfoxide rhGH, with no unknown peaks. Using a cell proliferation assay, the biological activities of the isolated products of SR–rhGH degradation were found to be equivalent to those of native hGH, as determined by comparison with a National Institute for Biological Standards and Control standard. In conclusion, SR–rhGH is structurally and functionally stable and maintains the intactness of rhGH.     

hGH单克隆抗体的筛选及双抗体夹心ELISA检测方法的建立

采用杂交瘤法制备单克隆抗体,并用辛酸-硫酸铵法纯化单抗,通过ELISA方法和Western blotting测定抗体的效价与特异性,并进行抗体类型、相对亲和力测定;应用纯化的单抗建立hGH双抗体夹心ELISA检测方法。筛选出两株可以稳定分泌抗hGH单抗的杂交瘤细胞株,分别命名为3E11、2G9,抗体类型均为IgG1,抗体滴度均可达10-10,特异性好,相对亲和力高,以筛选到的两株单抗建立的双抗夹心ELISA法线性范围为0.09～1.5625ng/mL,R2>0.9,灵敏度为0.09ng/mL。筛选出高效抗hGH的单抗,并建立了hGH双抗体夹心ELISA检测方法。     

Production of human growth hormone in transgenic rice seeds: co-introduction of RNA interference cassette for suppressing the gene expression of endogenous storage proteins

Rice seeds are potentially useful hosts for the production of pharmaceutical proteins. However, low yields of recombinant proteins have been observed in many cases because recombinant proteins compete with endogenous storage proteins. Therefore, we attempt to suppress endogenous seed storage proteins by RNA interference (RNAi) to develop rice seeds as a more efficient protein expression system. In this study, human growth hormone (hGH) was expressed in transgenic rice seeds using an endosperm-specific promoter from a 10 kDa rice prolamin gene. In addition, an RNAi cassette for reduction of endogenous storage protein expressions was inserted into the hGH expression construct. Using this system, the expression levels of 13 kDa prolamin and glutelin were effectively suppressed and hGH polypeptides accumulated to 470 μg/g dry weight at the maximum level in transgenic rice seeds. These results suggest that the suppression of endogenous protein gene expression by RNAi could be of great utility for increasing transgene products.     

Combination of Competitive Quantitative PCR and Constant-Denaturant Capillary Electrophoresis for High-Resolution Detection and Enumeration of Microbial Cells

A novel quantitative PCR (QPCR) approach, which combines competitive PCR with constant-denaturant capillary electrophoresis (CDCE), was adapted for enumerating microbial cells in environmental samples using the marine nanoflagellate Cafeteria roenbergensis as a model organism. Competitive PCR has been used successfully for quantification of DNA in environmental samples. However, this technique is labor intensive, and its accuracy is dependent on an internal competitor, which must possess the same amplification efficiency as the target yet can be easily discriminated from the target DNA. The use of CDCE circumvented these problems, as its high resolution permitted the use of an internal competitor which differed from the target DNA fragment by a single base and thus ensured that both sequences could be amplified with equal efficiency. The sensitivity of CDCE also enabled specific and precise detection of sequences over a broad range of concentrations. The combined competitive QPCR and CDCE approach accurately enumerated C. roenbergensis cells in eutrophic, coastal seawater at abundances ranging from approximately 10 to 10⁴ cells ml⁻¹. The QPCR cell estimates were confirmed by fluorescent in situ hybridization counts, but estimates of samples with <50 cells ml⁻¹ by QPCR were less variable. This novel approach extends the usefulness of competitive QPCR by demonstrating its ability to reliably enumerate microorganisms at a range of environmentally relevant cell concentrations in complex aquatic samples.     

Detection of Clostridium proteoclasticum and Closely Related Strains in the Rumen by Competitive PCR

A competitive PCR technique was used to enumerate the proteolytic bacterium Clostridium proteoclasticum from the rumen. A PCR primer, which circumscribes this organism and several closely related strains, was designed for a variable region within their 16S rRNA genes and was used in conjunction with a universal forward primer. This primer pair was tested for specificity against 85 ruminal bacterial strains. An internal control DNA was constructed for use in competitive PCRs and was shown to amplify under the same reaction conditions and with the same amplification efficiency as the target DNA. DNA from a known number of C. proteoclasticum cells was coamplified with the internal control to construct a standard curve. Rumen samples were collected from eight dairy cows fed four diets in rotation: high nitrogen, high nitrogen supplemented with carbohydrate, low nitrogen, and low nitrogen supplemented with carbohydrate. DNA extracted from these and spiked with internal control DNA was amplified with the C. proteoclasticum primer pair. The relative intensities of the PCR products were used to quantitate the numbers of C. proteoclasticum cell equivalents from the rumen samples. The numbers ranged from 2.01 × 10⁶ ml⁻¹ to 3.12 × 10⁷ ml⁻¹. There was no significant effect on the numbers of C. proteoclasticum detected in rumen samples among cows fed the four diets. The utility of the competitive PCR approach for quantifying ruminal bacterial populations in vivo and the occurrence of C. proteoclasticum in forage-fed dairy cows are discussed.     

Prokaryotic overexpression of TEV–rhGH and characterization of its polyclonal antibody

Recombinant protein technology represents one of the best solutions to achieve rapid, efficient, and cost-effective protein expression and purification of therapeutic proteins. Growth hormone (GH) is an excellent example of these proteins used in the therapy of hormone deficiencies. In this work, a plasmid, pRSET–TEV–rhGH, has been constructed to overexpress recombinant human GH (rhGH) by cloning its gene downstream of an N-terminal 6 × His-tagged polypeptide (43 aa) in the T7 promoter-plasmid pRSET. This polypeptide was cleavable by means of the integrated recognition site for the tobaccos etch virus (TEV) protease, resulting in an rhGH protein at an exact length and sequence. After IPTG induction, this plasmid effectively expressed TEV–rhGH protein (27 kDa) in the cytoplasm of Escherichia coli, which accumulated in the form of inclusion bodies. The 6 × His-tagged protein, with a yield of ~ 150 mg/L of culture, was purified from the cell extract using metal affinity chromatography, as shown after SDS-PAGE blue staining, and was confirmed by immunoblotting using specific commercial monoclonal antibodies. In order to detect TEV–rhGH, in ELISA and immunoblotting, specific polyclonal antibody, with high titer (~ 10^− 5 fold dilution), was produced in a rabbit and purified using affinity chromatography. Preliminary tests have proved that TEV–rhGH protein and its specific purified IgG antibody could provide valuable tools for rhGH productive and diagnostic purposes.     

Development and Testing of a DNA Macroarray To Assess Nitrogenase (nifH) Gene Diversity

A DNA macroarray was developed and evaluated for its potential to distinguish variants of the dinitrogenase reductase (nifH) gene. Diverse nifH gene fragments amplified from a clone library were spotted onto nylon membranes. Amplified, biotinylated nifH fragments from individual clones or a natural picoplankton community were hybridized to the array and detected by chemiluminescence. A hybridization test with six individual targets mixed in equal proportions resulted in comparable relative signal intensities for the corresponding probes (standard deviation, 14%). When the targets were mixed in unequal concentrations, there was a predictable, but nonlinear, relationship between target concentration and relative signal intensity. Results implied a detection limit of roughly 13 pg of target ml⁻¹, a half-saturation of signal at 0.26 ng ml⁻¹, and a dynamic range of about 2 orders of magnitude. The threshold for cross-hybridization varied between 78 and 88% sequence identity. Hybridization patterns were reproducible with significant correlations between signal intensities of duplicate probes (r = 0.98, P < 0.0001, n = 88). A mixed nifH target amplified from a natural Chesapeake Bay water sample hybridized strongly to 6 of 88 total probes and weakly to 17 additional probes. The natural community results were well simulated (r = 0.941, P < 0.0001, n = 88) by hybridizing a defined mixture of six individual targets corresponding to the strongly hybridizing probes. Our results indicate that macroarray hybridization can be a highly reproducible, semiquantitative method for assessing the diversity of functional genes represented in mixed pools of PCR products amplified from the environment.