Molecular screening for alkane hydroxylase genes in Gram-negative and Gram-positive strains

We have developed highly degenerate oligonucleotides for polymerase chain reaction (PCR) amplification of genes related to the Pseudomonas oleovorans GPo1 and Acinetobacter sp. ADP1 alkane hydroxylases, based on a number of highly conserved sequence motifs. In all Gram-negative and in two out of three Gram-positive strains able to grow on medium- (C₆–C₁₁) or long-chain n -alkanes (C₁₂–C₁₆), PCR products of the expected size were obtained. The PCR fragments were cloned and sequenced and found to encode peptides with 43.2–93.8% sequence identity to the corresponding fragment of the P. oleovorans GPo1 alkane hydroxylase. Strains that were unable to grow on n -alkanes did not yield PCR products with homology to alkane hydroxylase genes. The alkane hydroxylase genes of Acinetobacter calcoaceticus EB104 and Pseudomonas putida P1 were cloned using the PCR products as probes. The two genes allow an alkane hydroxylase-negative mutant of Acinetobacter sp. ADP1 and an Escherichia coli recombinant containing all P. oleovorans alk genes except alkB , respectively, to grow on n -alkanes, showing that the cloned genes do indeed encode alkane hydroxylases.     

Alkane hydroxylase genes in psychrophile genomes and the potential for cold active catalysis

Background

Psychrophiles are presumed to play a large role in the catabolism of alkanes and other components of crude oil in natural low temperature environments. In this study we analyzed the functional diversity of genes for alkane hydroxylases, the enzymes responsible for converting alkanes to more labile alcohols, as found in the genomes of nineteen psychrophiles for which alkane degradation has not been reported. To identify possible mechanisms of low temperature optimization we compared putative alkane hydroxylases from these psychrophiles with homologues from nineteen taxonomically related mesophilic strains.

Results

Seven of the analyzed psychrophile genomes contained a total of 27 candidate alkane hydroxylase genes, only two of which are currently annotated as alkane hydroxylase. These candidates were mostly related to the AlkB and cytochrome p450 alkane hydroxylases, but several homologues of the LadA and AlmA enzymes, significant for their ability to degrade long-chain alkanes, were also detected. These putative alkane hydroxylases showed significant differences in primary structure from their mesophile homologues, with preferences for specific amino acids and increased flexibility on loops, bends, and α-helices.

Conclusion

A focused analysis on psychrophile genomes led to discovery of numerous candidate alkane hydroxylase genes not currently annotated as alkane hydroxylase. Gene products show signs of optimization to low temperature, including regions of increased flexibility and amino acid preferences typical of psychrophilic proteins. These findings are consistent with observations of microbial degradation of crude oil in cold environments and identify proteins that can be targeted in rate studies and in the design of molecular tools for low temperature bioremediation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1120) contains supplementary material, which is available to authorized users.     

Studies on pulmonary aryl hydrocarbon hydroxylase activity in inbred strains of mice.

Pulmonary and hepatic levels of aryl hydrocarbon hydroxylase (AHH) were studied in inbred strains of mice following intratracheal (i.t.) instillation of 3-methylcholanthrene (MCA). I.t. instillation of 188 mug MCA in sterile 0.2% gelatin in saline resulted in preferential induction of pulmonary AHH. After treatment with this dose of MCA, the pulmonary AHH levels of strains C57BL/6Cum, C57BL/6J, BALB/cMai, C3H/fMai, and C57L/J were observed to be induced within 24 h after treatment. Strains DBA/2Cum, AKR/J, SJL/J, DBA/2J and RF/J expressed no such increase. At a dose of 500 mug MCA, the pulmonary tissue of DBA/2 mice did express a 4-fold increase. This increase in AHH was determined to be quite different from the increase observed in C57BL/6 mice by: (1) specific activity of the enzymes, (2) genetic regulation, (3) susceptibility to inhibition by 7,8-benzoflavone, and (4) spectral properties of the associated cytochromes. It was of major importance that induction of pulmonary AHH was observed to be regulated by a single dominant gene in crosses involving the C57BL/6Cum and DBA/2Cum strains of mice. Results were discussed with the view in mind that these genetically regulated levels of AHH may play a role in susceptibility to cancers induced by polycyclic aromatic hydrocarbon carcinogens.     

Oncogene homologues in yeast

Two different yeasts have a number of genes bearing striking structural and functional homologies to mammalian oncogenes. In yeast these genes are involved in the control of proliferation and early steps in the cell cycle. Many have putative protein kinase activity and some have been shown to control the activity of the enzyme adenylate cyclase which synthesizes cyclic AMP. Mutant forms of these yeast genes have oncogenic activity in mammalian cells.     

Sortase enzymes in Gram-positive bacteria

In Gram-positive bacteria proteins are displayed on the cell surface using sortase enzymes. These cysteine transpeptidases join proteins bearing an appropriate sorting signal to strategically positioned amino groups on the cell surface. Working alone, or in concert with other enzymes, sortases either attach proteins to the cross-bridge peptide of the cell wall or they link proteins together to form pili. Because surface proteins play a fundamental role in microbial physiology and are frequently virulence factors, sortase enzymes have been intensely studied since their discovery a little more than a decade ago. Based on their primary sequences and functions sortases can be partitioned into distinct families called class A to F enzymes. Most bacteria elaborate their surfaces using more than one type of sortase that function non-redundantly by recognizing unique sorting signals within their protein substrates. Here we review what is known about the functions of these enzymes and the molecular basis of catalysis. Particular emphasis is placed on 'pilin' specific class C sortases that construct structurally complex pili. Exciting new data have revealed that these enzymes are amazingly promiscuous in the substrates that they can employ and that there is a startling degree of diversity in their mechanism of action. We also review recent data that suggest that sortases are targeted to specific sites on the cell surface where they work with other sortases and accessory factors to properly function.     

Alkane hydroxylases involved in microbial alkane degradation

This review focuses on the role and distribution in the environment of alkane hydroxylases and their (potential) applications in bioremediation and biocatalysis. Alkane hydroxylases play an important role in the microbial degradation of oil, chlorinated hydrocarbons, fuel additives, and many other compounds. Environmental studies demonstrate the abundance of alkane degraders and have lead to the identification of many new species, including some that are (near)-obligate alkanotrophs. The availability of a growing collection of alkane hydroxylase gene sequences now allows estimations of the relative abundance of the different enzyme systems and the distribution of the host organisms.     

ICU病房G^＋菌谱及其耐药性连续9年监测

目的了解我院ICU病房分离菌中G^＋菌谱及其耐药情况,为临床防治G^＋菌感染提供依据。方法对ICU病房自1998年1月至2006年12月9年间所分离到的G^＋菌及其耐药性进行回顾性调查。结果9年间共分离获得G^＋菌408株,占总的23.2%（408/1755）。由1998年至2004年,G^＋菌分离率逐年增多,2004年后又有所下降。G^＋菌以金黄色葡萄球菌（SA）为主,占65.7%,其次为溶血葡萄球菌（SH,10.8%）、表皮葡萄球菌（SE,9.5%）。MRSA占SA的89.9%,MRSE占SE的92.3%。体外药敏试验结果显示主要G^＋菌均呈多重耐药特性,只有万古霉素对G^＋具有很强抗菌活性,敏感率达100%。结论ICU病房在所分离的G^＋菌中,耐甲氧西林葡萄球菌（MRS）所占比例很高,细菌呈多重耐药特性。我们应高度重视这一严重问题并尽一切可能预防院内感染和减少多重耐药菌的产生。     

Alkane distribution in epicuticular wax of epacridaceae

Alkane distribution pattern was determined in the epicuticular wax of leaves of 39 species and in the flower wax of three species of Epacridaceae. Uniform patterns were observed within some genera (Monotoca, Styphelia) whereas in others no common pattern was apparent. There was no difference between the alkane patterns of the two subfamilies Epacrideae and Styphelieae. The pattern was not affected by the presence of new growth, and there was no correlation with the season, habitat, climate, nature of soil, or the presence or absence of flowers.     

Association between Tph2 gene polymorphism, brain tryptophan hydroxylase activity and aggressiveness in mouse strains

The brain neurotransmitter serotonin is involved in the regulation of aggressive behavior. The main factor determining the brain serotonin level is the activity of the rate-limiting enzyme in the biosynthesis of the neurotransmitter--tryptophan hydroxylase isoform (TPH) 2 encoded by the Tph2 gene. Recently the C1473G single-nucleotide polymorphism in the Tph2 gene was reported. Here we study the C1473G polymorphism in 10 inbred mouse strains (C57BL/6J, AKR/J, DD/He, C3H/HeJ, YT/Y, BALB/cJLac, CC57BR/Mv and A/He) and demonstrate the association of the polymorphism with brain TPH activity and intermale aggressiveness. TPH activity in the midbrain of mice homozygous for the 1473C allele was higher than that in mice carrying 1473G alleles. A close association of the 1473C allele with increased number of attacks towards another male was found. The results support a link between the C1473G polymorphism in Tph2 gene, tryptophan hydroxylase activity and intensity of intermale aggression.     

Isolation of putative polyene-producing actinomycetes strains via PCR-based genome screening for polyene-specific hydroxylase genes

Polyene antibiotics, which include nystatin, pimaricin, amphotericin and candicidin, include a family of very promising antifungal polyketide compounds that are typically produced by soil actinomycetes. The presence of similar cytochrome P450 hydroxylase (CYP) genes in the biosynthetic gene clusters for these polyenes have been previously reported. Using this polyene, more than 200 independently isolated actinomycetes strains were screened by CYP-specific PCR. Four strains were isolated based on the presence of the expected size of the PCR-amplified DNA fragment in the chromosome. The nucleotide sequencing of the PCR-amplified DNA fragments showed that each of the four actinomycetes strains contained a highly homologous polyene-specific CYP gene. Each of the culture extracts from these four strains showed a typical polyene-like high-pressure liquid chromatography (HPLC) chromatogram profile, and strong antifungal activity against Candida albicans. This suggests that the polyene-specific PCR-guided genome screening approach is an efficient method for isolating potentially valuable polyene-producing actinomycetes.     

Distribution and evolution of the xylanase genes xynA and xynB and their homologues in strains of Butyrivibrio fibrisolvens.

The ruminal bacterium Butyrivibrio fibrisolvens is being engineered by the introduction of heterologous xylanase genes in an attempt to improve the utilization of plant material in ruminants. However, relatively little is known about the diversity and distribution of the native xylanase genes in strains of B. fibrisolvens. In order to identify the most appropriate hosts for such modifications, the xylanase genotypes of 28 strains from the three 16S ribosomal DNA (rDNA) subgroups of Butyrivibrio fibrisolvens have been investigated. Only 4 of the 20 strains from 16S rDNA group 2 contained homologues of the strain Bu49 xynA gene. However, these four xynA-containing strains, and two other group 2 strains, contained members of a second xylanase gene family clearly related to xynA (subfamily I). Homologues of xynB, a second previously described xylanase gene from B. fibrisolvens, were identified only in three of the seven group 1 strains and not in the group 2 and 3 strains. However, six of the group 1 strains contained one or more members of the two subfamilies of homologues of xynA. The distribution of genes and the nucleotide sequence relationships between the members of the two xynA subfamilies are consistent with the progenitor of all strains of B. fibrisolvens having contained a xynA subfamily I gene. Since many xylanolytic strains of B. fibrisolvens did not contain members of either of the xynA subfamilies or of the xynB family, at least one additional xylanase gene family remains to be identified in B. fibrisolvens.     

Comparison of Tir from enterohemorrahgic and enteropathogenic Escherichia coli strains: two homologues with distinct intracellular properties

Summary Tir of enteropathogenic Escherichia coli (EPEC) or enterohemorrahgic E. coil (EHEC) is translocated by a type III secretion system to the host cell membranes where it serves as a receptor for the binding of a second bacterial membrane protein. In response to the binding, EPEC Tir is phosphorylated at Tyr₄₇₄, and this phosphorylation is necessary for the signaling of pedestal formation. Tir of EHEC has no equivalent phosphorylation site but it is similarly needed for cytoskeleton rearrangement. How these two Tir molecules achieve their function by apparently different mechanisms is not completely clear. To examine their intrinsic differences, the two Tirs were expressed in HeLa cells and compared. Actin in complexes could be pelleted down from the lysate of cells expressing EHEC Tir but not EPEC Tir. By immunostaining, neither Tir molecule was found in phosphorylated state. In the cytoplasm, EHEC Tir was frequently found in fibrous structures whereas EPEC Tir was observed completely in a diffusive form. The determinant critical for the EHEC Tir fibrous formation was mapped to the C-terminal region of the molecule that deviates from the EPEC counterpart. This region may play a role in taking an alternative route different from Tyr₄₇₄ phosphorylation to transduce signals.     

原核生物微管蛋白家族研究进展

自从1992年确定细菌分裂的关键蛋白Fts Z属于微管蛋白家族以来,越来越多的细菌细胞骨架蛋白被发现。原核生物中的微管同源蛋白主要有Fts Z、Cet Z、Tub Z和Btub A/B等。它们与微管蛋白具有相似的三级结构,可以结合鸟嘌呤-5′-三磷酸(Guanosine triphosphate,GTP)自聚合成不同的线状原丝纤维结构:单线状原丝纤维、双螺旋纤维结构或聚集成束状结构,在细菌细胞分裂、维持细胞形态、质粒分离等诸多重要生理功能中起着重要作用。     

Ion-conducting channels in a Gram-positive bacterium

The patch-clamp technique was used to obtain information on the existence and properties of ion channels in giant protoplasts obtained from the Gram-positive bacterium Streptococcus faecalis. The membrane proved to contain a pore with numerous conductance states, ranging from 10 pS to several nanosiemens. Application of a slight pressure differential across the membrane resulted in the activation of the channel. The pressure sensitivity points to a relationship between this channel and one recently discovered in E.coli spheroplasts [(1987) Proc. Natl. Acad. Sci. USA 84, 2297–2301] suggesting that pores of this type might be widespread among prokaryotes.