Optimal reference genes for real-time quantitative PCR and the expression of sigma factors in Acidithiobacillus caldus under various conditions

AIMS

Acidithiobacillus caldus is an important sulphur-oxidizing bacterium that plays crucial roles in the bioleaching industry. This study aims to analyse the optimal reference gene for real-time quantitative PCR (RT-qPCR) under different conditions and investigate the transcription levels of the sigma factor genes in the stress response.

METHODS AND RESULTS

We selected six housekeeping genes and analysed them via RT-qPCR using two energy resources, under four stress conditions. Three statistical approaches BestKeeper, geNorm, and NormFinder were utilized to determine transcription stability of these reference genes. The gapdH gene was the best internal control gene using elemental sulphur as an energy resource and under heat stress, map was the best internal control gene under pH and osmotic stress, era was the best internal control gene for the K₂ S₄ O₆ energy resource, and rpoC was the best internal control gene under Cu²⁺ stress. Furthermore, the expressional levels of 11 sigma factors were analysed by RT-qPCR in the stress response.

CONCLUSIONS

Stable internal control genes for RT-qPCR analysis of A. caldus were determined, and the expression patterns of sigma factor genes of A. caldus were investigated.

SIGNIFICANCE AND IMPACT OF THE STUDY

The identification of the optimal reference gene and analysis of transcription levels of sigma factors in A. caldus can provide clues for reference gene selection and the study of sigma factor function.

First Report on the Occurrence of Cucumber mosaic virus on Fragaria ananassa in China

More than 20 viruses are known to infect strawberry (Fragaria ananassa), and a substantial number of these include new viruses identified since 2000 that can contribute to disease complexes (2). The most serious virus related losses in commercial strawberries are caused by aphid transmitted viruses (3,4,5). A survey was undertaken from 2012 to 2013 to investigate virus prevalence in commercial strawberries in rural areas of Hebei Province around Beijing, China, that were exhibiting virus symptoms. Visual observations revealed that the incidence of virus-like symptoms ranged from 30 to 50% of the plants and these symptoms included yellowing, leaf malformation, sometimes combined with severe stunting and deformed flowers or fruits. Leaf samples were tested for Strawberry vein banding virus (SVBV), Strawberry mottle virus (SMoV), Strawberry mild yellow edge virus (SMYEV), and Strawberry crinkle virus (SCV), which are the four most prevalent aphid-transmitted viruses in single or mixed infections (2). Testing was conducted by RT-PCR using total RNA extracted from fresh symptomatic strawberry leaves (3). SVBV was detected in 58 of 190 samples, but all of the samples tested negative for SMoV, SMYEV, and SCV. Aphids were present on many of the plants, so the samples were tested for Cucumber mosaic virus (CMV) because CMV is prevalent in Beijing gardens and farms, and recently had been shown to infect maize in China (5). This RT-PCR was carried out with the CMV primer pair CM420-F (5'-TGATTCTACCGTGTGGGTGA-3') and CM420-R (5'-CCGTAAGCTGGATGGACAAC-3') to amplify a portion of the capsid protein coding region and the conserved 3'non-translated regions of the genomic RNAs. This test revealed the presence of 43 CMV-positives out of 190 samples, and only 16 of these samples were co-infected with both SVBV and CMV. Samples infected with CMV only had leaf malformations and yellowing, while no CMV was found in symptomless samples. One of the amplified, CMV-specific DNA fragments was sequenced directly from the PCR product and showed 93.8% nucleotide sequence identity and 100% amino acid sequence identity to the CMV subgroup I (GenBank Accession No. D10538) (1). Subsequent ELISA tests for the CMV presence verified the RT-PCR results (Agdia, Elkhart, IN), and transmission electron microscopy observations revealed 28 nm spherical particles characteristic of CMV in strawberry samples tested positive for CMV. However, we were unable to detect either CMV or SVBV in 89 of the 169 samples from symptomatic plants, which suggested possible presence of the other pathogen(s). To the best of our knowledge, this is the first report of natural infections of CMV in strawberry plants. These data suggests that CMV is a potential threat to strawberry production. References: (1) M. Q. K. Andrew et al. Virus taxonomy: IXth Report of the ICTV, 970, Elsevier, 2012. (2) R. R. Martin and I. E. Tzanetakis. Plant Dis. 97:1358, 2013. (3) J. R. Thompson et al. J. Virol. Methods 111:85, 2003. (4) I. E. Tzanetakis et al. Plant Dis. 90:1343, 2006. (5) R. Wang et al. J. Phytopathol. 161: 880, 2013.

First Report of Potato Virus H on Solanum muricatum in China

Solanum muricatum, commonly known as pepino, pepino dulce, or tree melon, is a perennial shrub well known for its attractive, sweet, flavorful fruits and is frequently cultivated as an annual. It has gained increasing popularity in China and is grown as a cash crop in many provinces. S. muricatum belongs to the family Solanaceae and is closely related to tomato, eggplant, and potato. In 2012, during a study of serological relationships between PVH and PVM on potatoes, potato virus H (PVH) was detected serendipitously in symptomless pepino plantlets in Beijing, grown from tissue culture stocks. PVH is a recently discovered carlavirus reported from potato plants from Huhhot, Inner Mongolia Autonomous Region. Since then, it was found on potatoes in Yunnan, Hebei, Liaoning, Heilongjiang, and Xinjiang provinces. PVH induces mild symptoms with a slight leaf curl in systemic leaves, but most often it is almost symptomless or latent on potatoes (2). To confirm the presence of PVH on S. muricatum, surveys were conducted in 2012 and 2013 in Gansu, Yunnan, and Guangxi provinces and Beijing. Fruits and leaves were collected randomly from pepino plants displaying no obvious symptoms. For PVH detection, a combination of RT-PCR, genome sequencing and serological assays were used. RNAs extracted from fruits and leaves were amplified using RT-PCR with primer pairs PVHCPF and PVHCPR (2), and extracted samples were probed by Western blotting with the specific polyclonal antiserum against PVH (2). Among the 50 plants randomly collected, fruits and leaves of nine plants tested positive for PVH. Subsequently, an RT-PCR product of the expected size (2.6 kb) encompassing the triple-gene block, the capsid protein gene, and the cysteine-rich protein gene, was amplified with a specific primer pair (PVHB1F 5'-TGATGGAATTTACAAAAAC-3' and PVHUR 5'-CTTATGCGCATCTATCAATC-3'), and then cloned into pMD19-T (TaKaRa, Dalian, China) and sequenced (PVH-Pepino with GenBank Accession No. KF546312). Further sequence comparison showed that PVH-Pepino shared 91 to 98% nucleotide sequence identity in the genes mentioned above with those of the reported potato isolates PVH-Ho and PVH-YN (HM584819 and JQ904630, respectively). PVH-Pepino shared deduced amino acid identity of 98 to 99% in CP gene with PVH-Ho and PVH-YN, respectively, but only shared 57 to 67% amino acid identities with other reported carlaviruses (1,2). Thus, latent infection of PVH on S. muricatum was confirmed. To our knowledge, this is the first report of S. muricatum as a natural host of PVH. Our results suggest that PVH, as a new member of the genus Carlavirus, has a wider host range than originally expected. Potatoes and pepinos are crops widely grown in China. The fact that no symptoms were expressed by PVH in pepino plants (symptomless carrier) and only mild symptoms expressed by PVH in diseased potatoes makes detection and remediation of this disease more difficult. Although this finding does not show that PVH is economically important to pepino, this cannot be excluded in the presence of other viruses (2). References: (1) A. King et al. Page 881 in: Virus Taxonomy, Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, London, 2011. (2) Y. Y. Li et al. PLOS ONE 8(6):e69255, 2013.

Trichosanthes kirilowii: A New Host of Cucurbit mild mosaic virus in China

Chinese cucumber (Trichosanthes kirilowii Maxim.) is a type of perennial liana plant of the Cucurbitaceae family that is mainly distributed in East Asia and northern Australia. It is an important medicinal plant and commonly used in Chinese herbalism, where it is considered to be one of the 50 fundamental herbs (2). During the summer and autumn of 2012, T. kirilowii plants showing symptoms of mild mosaic on the upper leaves and bright yellow color on the lower leaves were observed in the Haidian district of Beijing, China. Recently similar symptoms induced by Cucurbit mild mosaic virus (CuMMV) on squash have been reported. CuMMV is a new member of the genus Fabavirus in the Comovirinae subfamily, discovered in China in 2006 (1). Total RNA was extracted from five leaf samples of independent plants and used for reverse transcription with an oligo (dT)₁₈ primer, followed by PCR with a pair of CuMMV virus-specific primers FaR₁3012F (5'-CGAGTGCGAGTTAGAAATTGGGATG-3') and FaR₁5783R (5'-TCACTTTGAGGTGATAAAACAATCC-3') to amplify a 2,772-bp fragment including RNA-dependent RNA polymerase (RdRp) coding region. The expected target fragment was obtained in all symptomatic plant samples but not from an asymptomatic plant. Nucleotide sequence comparison analysis showed that the virus isolated from T. kirilowii (GenBank Accession No. KC959843) had 95.33% nucleotide identity and 99.15% amino acid identity in the RdRp sequence with a CuMMV isolate from squash (GenBank Accession No. FJ194941) (1). In addition, symptomatic samples tested positive for CuMMV by Western blot using CuMMV small coat protein (SCP) specific polyclonal antibody (1). To our knowledge, this is the first report of T. kirilowii as natural host of CuMMV in China. The impact of CuMMV on T. kirilowii production remains to be determined; however, the extended host range for this virus suggests a potential threat of CuMMV to cucurbit crops in China. References: (1) S. W. Dong et al. Arch. Virol.157:597, 2012. (2) J. H. Hong et al. China Pharmacist 7:561, 2004.

Studies on interaction of cucurbit aphid-borne yellow virus proteins using yeast two-hybrid system and bimolecular fluorescence complementation

In this article, yeast two-hybrid system (YTHS) and bimolecular fluorescence complementation (BiFC) were used to analyze the interactions of cucurbit aphid-borne yellows virus (CABYV)-encoded proteins. P0, P1, P1-2, P3, P4, and P5 were tested by YTHS in all possible pairwise combinations, and only P3/P3 interaction was detected. Results obtained by BiFC further confirmed the self-interaction of P3, and the subcellular localization of reconstituted YFP fluorescence was observed mainly in nuclei of Nicotiana benthamiana leaf epidermal cells. Domains involved in P3/P3 self-interaction were analyzed by YTHS and BiFC using deletion mutants. The results showed that R domain (residues 1-61) in the N-terminus could self-interact, and it also interacted with the S domain (residues 62-199) in the C-terminus of P3. The present work would serve as a molecular basis for further characterization of CABYV proteins, and the regions involved in P3/P3 self-interaction could provide the clue for understanding the capsid assembly pathway of CABYV.

Reactive oxygen species in rats with chronic post-ischemia pain

BACKGROUND

An emerging theme in the study of the pathophysiology of persistent pain is the role of reactive oxygen species (ROS). In the present study, we examined the hypothesis that the exogenous supply of antioxidant drugs during peri-reperfusion would attenuate pain induced by ischemia/reperfusion (IR) injury. We investigated the analgesic effects of three antioxidants administered during peri-reperfusion using an animal model of complex regional pain syndrome-type I consisting of chronic post-ischemia pain (CPIP) of the hind paw.

METHODS

Application of a tight-fitting tourniquet for a period of 3 h produced CPIP in male Sprague-Dawley rats. Low-dose allopurinol (4 mg/kg), high-dose allopurinol (40 mg/kg), superoxide dismutase (SOD, 4000 U/kg), N-nitro-L-arginine methyl ester (L-NAME, 10 mg/kg), or SOD (4000 U/kg)+L-NAME (10 mg/kg) was administered intraperitoneally just after tourniquet application and at 1 and 2 days after reperfusion for 3 days. The effects of antioxidants in rats were investigated using mechanical and cold stimuli. Each group consisted of seven rats.

RESULTS

Allopurinol caused significant alleviation in mechanical and cold allodynia for a period of 4 weeks in rats with CPIP. Both SOD and L-NAME, which were used to investigate the roles of superoxide (O2(-)) and nitric oxide (NO) in pain, also attenuated neuropathic-like pain symptoms in rats for 4 weeks.

CONCLUSIONS

Our findings suggest that O2(-) and NO mediate IR injury-induced chronic pain, and that ROS scavengers administered during the peri-reperfusion period have long-term analgesic effects.

Structural and functional characterization of IS679 and IS66-family elements

A new insertion sequence (IS) element, IS679 (2,704 bp in length), has been identified in plasmid pB171 of enteropathogenic Escherichia coli B171. IS679 has imperfect 25-bp terminal inverted repeats (IRs) and three open reading frames (ORFs) (here called tnpA, tnpB, and tnpC). A plasmid carrying a composite transposon (Tn679) with the kanamycin resistance gene flanked by an intact IS679 sequence and an IS679 fragment with only IRR (IR on the right) was constructed to clarify the transposition activity of IS679. A transposition assay done with a mating system showed that Tn679 could transpose at a high frequency to the F plasmid derivative used as the target. On transposition, Tn679 duplicated an 8-bp sequence at the target site. Tn679 derivatives with a deletion in each ORF of IS679 did not transpose, finding indicative that all three IS679 ORFs are essential for transposition. The tnpA and tnpC products appear to have the amino acid sequence motif characteristic of most transposases. A homology search of the databases found that a total of 25 elements homologous to IS679 are present in Agrobacterium, Escherichia, Rhizobium, Pseudomonas, and Vibrio spp., providing evidence that the elements are widespread in gram-negative bacteria. We found that these elements belong to the IS66 family, as do other elements, including nine not previously reported. Almost all of the elements have IRs similar to those in IS679 and, like IS679, most appear to have duplicated an 8-bp sequence at the target site on transposition. These elements have three ORFs corresponding to those in IS679, but many have a mutation(s) in an ORF(s). In almost all of the elements, tnpB is located in the -1 frame relative to tnpA, such that the initiation codon of tnpB overlaps the TGA termination codon of tnpA. In contrast, tnpC, separated from tnpB by a space of ca. 20 bp, is located in any one of three frames relative to tnpB. No common structural features were found around the intergenic regions, indicating that the three ORFs are expressed by translational coupling but not by translational frameshifting.

Identification and distribution of new insertion sequences in the genome of alkaliphilic Bacillus halodurans C-125

Fifteen kinds of new insertion sequences (ISs), IS641 to IS643, IS650 to IS658, IS660, IS662, and IS663, and a group II intron (Bh.Int) were identified in the 4,202,352-bp genome of alkaliphilic Bacillus halodurans C-125. Out of 120 ISs identified in the C-125 genome, 29 were truncated, indicating the occurrence of internal rearrangements of the genome. The ISs other than IS650, IS653, IS660, and IS663 generated a 2- to 9-bp duplication of the target site sequence, and the ISs other than IS650, IS653, and IS657 carry 14- to 64-bp inverted repeats. Sequence analysis revealed that six kinds of ISs (IS642, IS643, IS654, IS655, IS657, and IS658) belong to a separate IS family (IS630, IS21, IS256, IS3, IS200/IS605, and IS30, respectively) as a new member. Also, IS651 and IS652 were characterized as new members of the ISL3 family. Significant similarity was found between the transposase (Tpase) sequences between IS650 and IS653 (78.2%), IS651 and IS652 (56.3%), IS656 and IS662 (71.0%), and IS660 and IS663 (44.5%), but the others showed no similarity to one another. Tpases in 28 members of IS651 in the C-125 genome were found to have become diversified. Most of the IS elements widely distributed throughout the genome were inserted in noncoding regions, although some genes, such as those coding for an ATP-binding cassette transporter/permease, a response regulator, and L-indole 2-dehydrogenase, have been mutated through the insertion of IS elements. It is evident, however, that not all IS elements have transposed and caused rearrangements of the genome in the past 17 years during which strain C-125 was subcultured under neutral and alkaline conditions.

Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12

Escherichia coli O157:H7 is a major food-borne infectious pathogen that causes diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome. Here we report the complete chromosome sequence of an O157:H7 strain isolated from the Sakai outbreak, and the results of genomic comparison with a benign laboratory strain, K-12 MG1655. The chromosome is 5.5 Mb in size, 859 Kb larger than that of K-12. We identified a 4.1-Mb sequence highly conserved between the two strains, which may represent the fundamental backbone of the E. coli chromosome. The remaining 1.4-Mb sequence comprises of O157:H7-specific sequences, most of which are horizontally transferred foreign DNAs. The predominant roles of bacteriophages in the emergence of O157:H7 is evident by the presence of 24 prophages and prophage-like elements that occupy more than half of the O157:H7-specific sequences. The O157:H7 chromosome encodes 1632 proteins and 20 tRNAs that are not present in K-12. Among these, at least 131 proteins are assumed to have virulence-related functions. Genome-wide codon usage analysis suggested that the O157:H7-specific tRNAs are involved in the efficient expression of the strain-specific genes. A complete set of the genes specific to O157:H7 presented here sheds new insight into the pathogenicity and the physiology of O157:H7, and will open a way to fully understand the molecular mechanisms underlying the O157:H7 infection.

New transposable elements identified as insertions in rice transposon Tnr1

Tnr1 (235 bp long) is a transposable element in rice. Polymerase chain reactions (PCRs) done with a primer(s) that hybridizes to terminal inverted repeat sequences (TIRs) of Tnr1 detected new Tnr1 members with one or two insertions in rice genomes. Six identified insertion sequences (Tnr4, Tnr5, Tnr11, Tnr12, Tnr13 and RIRE9) did not have extensive homology to known transposable elements, rather they had structural features characteristic of transposable elements. Tnr4 (1767 bp long) had imperfect 64-bp TIRs and appeared to generate duplication of a 9-bp sequence at the target site. However, the TIR sequences were not homologous to those of known transposable elements, indicative that Tnr4 is a new transposable element. Tnr5 (209 bp long) had imperfect 46-bp TIRs and appeared to generate duplication of sequence TTA like that of some elements of the Tourist family. Tnr11 (811 bp long) had 73-bp TIRs with significant homology to those of Tnr1 and Stowaway and appeared to generate duplication of sequence TA, indicative that Tnr11 is a transposable element of the Tnr1/Stowaway family. Tnr12 (2426 bp long) carried perfect 9-bp TIRs, which began with 5'-CACTA- -3' from both ends and appeared to generate duplication of a 3-bp target sequence, indicative that Tnr12 is a transposable element of the En/Spm family. Tnr13 (347 bp long) had 31-bp TIRs and appeared to generate duplication of an 8-bp target sequence. Two sequences, one the transposon-like element Crackle, had partial homology in the Tnr13 ends. All five insertions appear to be defective elements derived from autonomous ones encoding the transposase gene. All had characteristic tandem repeat sequences which may be recognized by transposase. The sixth insertion sequence, named RIRE9 (3852 bp long), which begins with 5'-TG- -3' and ends with 5'- -CA-3', appeared to generate duplication of a 5-bp target sequence. These and other structural features indicate that this insertion is a solo LTR (long terminal repeat) of a retrotransposon. The transposable elements described above could be identified as insertions into Tnr1, which do not deleteriously affect the growth of rice cells.

Complete DNA sequence and structural analysis of the enteropathogenic Escherichia coli adherence factor plasmid

The complete nucleotide sequence and organization of the enteropathogenic Escherichia coli (EPEC) adherence factor (EAF) plasmid of EPEC strain B171 (O111:NM) were determined. The EAF plasmid encodes two known virulence-related operons, the bfp operon, which is composed of genes necessary for biosynthesis of bundle-forming pili, and the bfpTVW (perABC) operon, composed of regulatory genes required for bfp transcription and also for transcriptional activation of the eae gene in the LEE pathogenicity island on the EPEC chromosome. The 69-kb EAF plasmid, henceforth designated pB171, contains, besides the bfp and bfpTVW (perABC) operons, potential virulence-associated genes, plasmid replication and maintenance genes, and many insertion sequence elements. Of the newly identified open reading frames (ORFs), two which comprise a single operon had the potential to encode proteins with high similarity to a C-terminal region of ToxB whose coding sequence is located on pO157, a large plasmid harbored by enterohemorrhagic E. coli. Another ORF, located between the bfp and bfpTVW operons, showed high similarity with trcA, a bfpT-regulated chaperone-like protein gene of EPEC. Two sites were found to be putative replication regions: one similar to RepFIIA of p307 or F, and the other similar to RepFIB of R100 (NR1). In addition, we identified a third region that contains plasmid maintenance genes. Insertion elements were scattered throughout the plasmid, indicating the mosaic nature of the EAF plasmid and suggesting evolutionary events by which virulence genes may have been obtained.

Complete nucleotide sequences of 93-kb and 3.3-kb plasmids of an enterohemorrhagic Escherichia coli O157:H7 derived from Sakai outbreak

Enterohemorrhagic Escherichia coli (EHEC) O157:H7, derived from an outbreak in Sakai city, Japan in 1996, possesses two kinds of plasmids: a 93-kb plasmid termed pO157, found in clinical EHEC isolates world-wide and a 3.3-kb plasmid termed pOSAK1, prevalent in EHEC strains isolated in Japan. Complete nucleotide sequences of both plasmids have been determined, and the putative functions of the encoded proteins and the cis-acting DNA sequences have been analyzed. pO157 shares strikingly similar genes and DNA sequences with F-factor and the transmissible drug-resistant plasmid R100 for DNA replication, copy number control, plasmid segregation, conjugative functions and stable maintenance in the host, although it is defective in DNA transfer by conjugation due to the truncation and deletion of the required genes and DNA sequences. In addition, it encodes several proteins implicated in EHEC pathogenicity such as an EHEC hemolysin (HlyA), a catalase-peroxidase (KatP), a serine protease (EspP) and type II secretion system. pOSAK1 possesses a ColE1-like replication system, and the DNA sequence is extremely similar to that of a drug-resistant plasmid, NTP16, derived from Salmonella typhimurium except that it lacks drug resistance transposons.