Structural Gene Sequences Research Articles

Evaluating the effectiveness of rhizobacteria producing 1-aminocyclopropane-1-carboxylic acid deaminase in inhibiting tumor formation by Agrobacterium tumefaciens

Crown gall is one of the most dangerous bacterial diseases affecting the production of fruit tree nurseries in Egypt and many countries of the world. In the present study, ten isolates of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing rhizobacteria were isolated from the rhizosphere of apricot (Prunus armeniaca L.) and plum (Prunus domestica L.) trees to evaluate their ability to decrease tumor formation by Agrobacterium tumefaciens (synonym Rhizobium radiobacter). The ten isolates were identified as Pseudomonas strains based on 16S rRNA gene sequence analysis and deduced protein sequences obtained from a partial ACC deaminase structural gene (acdS) sequence. Co-inoculating castor bean (Ricinus communis L.) and kalanchoe (Kalanchoe sp.) plants with A. tumefaciens and four ACC deaminase-producing Pseudomonas isolates decreased tumor formation. However, six ACC deaminase-producing Pseudomonas isolates produced varying results in these two plant species. The results showed that isolates of Pseudomonas vancouverensis reduced tumor formation when co-inoculated with A. tumefaciens in castor bean and kalanchoe plants. However, the isolate P. putida inhibited tumor formation in castor bean plants but did not achieve the same effect in kalanchoe plants. Additionally, isolates of P. frederiksbergensis and P. kilonensis decreased tumor formation in kalanchoe plants while increasing tumor formation in castor bean plants. The results showed that ACC deaminase-producing P. vancouverensis is a promising biocontrol agent against A. tumefaciens.

Identification and epidemiological study of an uncultured flavivirus from ticks using viral metagenomics and pseudoinfectious viral particles

During their blood-feeding process, ticks are known to transmit various viruses to vertebrates, including humans. Recent viral metagenomic analyses using next-generation sequencing (NGS) have revealed that blood-feeding arthropods like ticks harbor a large diversity of viruses. However, many of these viruses have not been isolated or cultured, and their basic characteristics remain unknown. This study aimed to present the identification of a difficult-to-culture virus in ticks using NGS and to understand its epidemic dynamics using molecular biology techniques. During routine tick-borne virus surveillance in Japan, an unknown flaviviral sequence was detected via virome analysis of host-questing ticks. Similar viral sequences have been detected in the sera of sika deer and wild boars in Japan, and this virus was tentatively named the Saruyama virus (SAYAV). Because SAYAV did not propagate in any cultured cells tested, single-round infectious virus particles (SRIP) were generated based on its structural protein gene sequence utilizing a yellow fever virus-based replicon system to understand its nationwide endemic status. Seroepidemiological studies using SRIP as antigens have demonstrated the presence of neutralizing antibodies against SAYAV in sika deer and wild boar captured at several locations in Japan, suggesting that SAYAV is endemic throughout Japan. Phylogenetic analyses have revealed that SAYAV forms a sister clade with the Orthoflavivirus genus, which includes important mosquito- and tick-borne pathogenic viruses. This shows that SAYAV evolved into a lineage independent of the known orthoflaviviruses. This study demonstrates a unique approach for understanding the epidemiology of uncultured viruses by combining viral metagenomics and pseudoinfectious viral particles.

COVID-19 Genomic Surveillance in Bangui (Central African Republic) Reveals a Landscape of Circulating Variants Linked to Validated Antiviral Targets of SARS-CoV-2 Proteome.

Since its outbreak, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread rapidly, causing the Coronavirus Disease 19 (COVID-19) pandemic. Even with the vaccines' administration, the virus continued to circulate due to inequal access to prevention and therapeutic measures in African countries. Information about COVID-19 in Africa has been limited and contradictory, and thus regional studies are important. On this premise, we conducted a genomic surveillance study about COVID-19 lineages circulating in Bangui, Central African Republic (CAR). We collected 2687 nasopharyngeal samples at four checkpoints in Bangui from 2 to 22 July 2021. Fifty-three samples tested positive for SARS-CoV-2, and viral genomes were sequenced to look for the presence of different viral strains. We performed phylogenetic analysis and described the lineage landscape of SARS-CoV-2 circulating in the CAR along 15 months of pandemics and in Africa during the study period, finding the Delta variant as the predominant Variant of Concern (VoC). The deduced aminoacidic sequences of structural and non-structural genes were determined and compared to reference and reported isolates from Africa. Despite the limited number of positive samples obtained, this study provides valuable information about COVID-19 evolution at the regional level and allows for a better understanding of SARS-CoV-2 circulation in the CAR.

Genomic characterization and evolutionary analysis of dengue virus from Aedes mosquitoes in Telangana, India.

Entomological surveillance for mosquito-borne viruses is vital for monitoring disease transmission and vector control programs. The vector control program is reliant not only on vector density but also on the timely detection of mosquito-borne infections. In the present study, we conducted an entomological surveillance in different locations of Hyderabad, Telangana, India during 2017-2018 and the collected mosquitoes were screened for dengue virus. Reverse transcriptase polymerase chain reaction (RT-PCR) was used for the identification and serotyping of the dengue virus. Bioinformatics analysis was performed using Mega 6.0 software. Followed by phylogenetic analysis, which was based on CprM structural genome sequence, was performed by using the Maximum-Likelihood method. The TaqMan RT-PCR assay was used to analyze the serotypes of 25 pools of Aedes mosquitoes and found that all four serotypes are circulating in Telangana. DENV1 (50%) was the most commonly detected serotype followed by DENV2 (16.6%), DENV3 (25%), and DENV4 (8.3%). Moreover, DENV1 has the highest MIR (16 per 1000 mosquitoes) compared with DENV2, 3, and 4. The CprM structural gene sequence was used for phylogenetic analysis, revealing that all four strains have a close relationship with strains isolated from India, Pakistan, China and Thailand. Similarly, two variations in amino acid sequence DENV1 at position 43 (K-R) and 86 (S-T) and a single mutation DENV2 at 111 amino acid position were observed. The results of the study provide an in-depth transmission dynamic of the dengue virus and persistence of this emerging pathogen in Telangana, India that needs appropriate prevention programs.

Nisin variants from Streptococcus and Staphylococcus successfully express in NZ9800.

Increases in antimicrobial resistance have meant that the antimicrobial potential of lantibiotics is now being investigated irrespective of the nature of the producing organism. The aim of this study was to investigate whether natural nisin variants produced by non-Generally Recognized as Safe (GRAS) strains, such as nisin H, nisin J and nisin P, could be expressed in a well-characterized GRAS host. This study involved cloning the nisin A promoter and leader sequence fused to nisin H, nisin J or nisin P structural gene sequences originally produced by Streptococcus hyointestinalis DPC 6484, Staphylococcus capitis APC 2923 and Streptococcus agalactiae DPC 7040, respectively. This resulted in their expression in Lactococcus lactis NZ9800, a genetically modified strain that does not produce nisin A. Induction of the nisin controlled gene expression system demonstrates that these three nisin variants could be acted on by nisin A machinery provided by the host strain. Describes the first successful heterologous production of three natural nisin variants by a GRAS strain, and demonstrates how such systems could be harnessed not only for lantibiotic production but also in the expansion of their structural diversity and development for use as future biotherapeutics.

Production of Bacteriocin by Various Strains of Pediococcus acidilacti during Batch Fermentation and Identification of the Pediocin Structural Genes

Bacteriocins are antimicrobial peptides produced by certain bacteria that can be alternatives to traditional antibiotics. This study aimed at evaluating large-scale bacteriocin production by the Pediococcus acidilactici strains in batch fermentation and to analyze the pediocin structural gene (papA) by bioinformatic methods. The fermentation using bacterial strains was carried out in Sartorius Biostat A-Plus Bioreactor, and the bacteriocin production was tested on Listeria innocua as a result of 24 h fermentation. The pediocin structural gene papA was amplified, and the amplicons of each strain were sequenced and analyzed to assess the secondary structure of pediocin and related metabolic pathways. It was shown that the papA structural gene sequence is a conserved region. All strains with a papA amplicon synthesis exhibited active bacteriocin synthesis Keywords: fermentation, Pediococcus acidilactici, purified bacteriocin, pediocin structural gene Funding - The authors acknowledge the grant support by the National Institutes of Molecular Biology and Biotechnology (BIOTECH), Laguna, Philippines.

Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses.

Sorghum (Sorghum bicolor) is cultivated worldwide for food, bioethanol, and fodder production. Although nitrogen fixation in sorghum has been studied since the 1970s, N2-fixing bacteria have not been widely examined in field-grown sorghum plants because the identification of functional diazotrophs depends on the culture method used. The aim of this study was to identify functional N2-fixing bacteria associated with field-grown sorghum by using “omics” approaches. Four lines of sorghum (KM1, KM2, KM4, and KM5) were grown in a field in Fukushima, Japan. The nitrogen-fixing activities of the roots, leaves, and stems were evaluated by acetylene reduction and 15N2-feeding assays. The highest nitrogen-fixing activities were detected in the roots of lines KM1 and KM2 at the late growth stage. Bacterial cells extracted from KM1 and KM2 roots were analyzed by metagenome, proteome, and isolation approaches and their DNA was isolated and sequenced. Nitrogenase structural gene sequences in the metagenome sequences were retrieved using two nitrogenase databases. Most sequences were assigned to nifHDK of Bradyrhizobium species, including non-nodulating Bradyrhizobium sp. S23321 and photosynthetic B. oligotrophicum S58T. Amplicon sequence and metagenome analysis revealed a relatively higher abundance (2.9–3.6%) of Bradyrhizobium in the roots. Proteome analysis indicated that three NifHDK proteins of Bradyrhizobium species were consistently detected across sample replicates. By using oligotrophic media, we purified eight bradyrhizobial isolates. Among them, two bradyrhizobial isolates possessed 16S rRNA and nif genes similar to those in S23321 and S58T which were predicted as functional diazotrophs by omics approaches. Both free-living cells of the isolates expressed N2-fixing activity in a semi-solid medium according to an acetylene reduction assay. These results suggest that major functional N2-fixing bacteria in sorghum roots are unique bradyrhizobia that resemble photosynthetic B. oligotrophicum S58T and non-nodulating Bradyrhizobium sp. S23321. Based on our findings, we discuss the N2-fixing activity level of sorghum plants, phylogenetic and genomic comparison with diazotrophic bacteria in other crops, and Bradyrhizobium diversity in N2 fixation and nodulation.

Complete Genome Sequences of Three Sub-genotype 2.1b Isolates of Classical Swine Fever Virus in China.

IntroductionClassical swine fever (CSF) has caused severe economic losses in pig production in many countries. Recent CSF outbreaks in China are mainly associated with sub-genotype 2.1 of CSF virus (CSFV). Although there is abundant information regarding 2.1 isolates, few data are available on whole-genome analysis.Material and MethodsThe biological and genome characteristics of three recently emerged Chinese CSFV isolates, i.e. SD2014-1, SD2014-2, and SD2014-3, were fully analysed.ResultsSequence analysis showed that the isolates shared 83.4%–95.0% nucleotide identity with eight other CSFV isolates. In addition, the 5′ untranslated region (5′UTR) and the non-structural (NS) proteins NS3, NS4A, and NS4B were more conserved than other regions of the genome. Phylogenetic analysis based on the complete genome sequences or full-length structural protein E2 gene sequences revealed that the three isolates belonged to sub-genotype 2.1b. In addition, several unique molecular characteristics of the 5′UTR, 3′UTR, and E2 were identified.ConclusionThe genomic variations of the three isolates will support further analysis of virulence determinants and the evolutionary trend of CSFV.

Enhancing heterologous protection in pigs vaccinated with chimeric porcine reproductive and respiratory syndrome virus containing the full-length sequences of shuffled structural genes of multiple heterologous strains

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of arguably the most economically important global swine disease. The extensive genetic variation of PRRSV strains is a major obstacle for heterologous protection of current vaccines. Previously, we constructed a panel of chimeric viruses containing only the ectodomain sequences of DNA-shuffled structural genes of different PRRSV strains in the backbone of a commercial vaccine, and found that one chimeric virus had an improved cross-protection efficacy. In this present study, to further enhance the cross-protective efficacy against heterologous strains, we constructed a novel chimeric virus VR2385-S3456 containing the full-length sequences of shuffled structural genes (ORFs 3-6) from 6 heterologous PRRSV strains in the backbone of PRRSV strain VR2385. We showed that the chimeric virus VR2385-S3456 induced a high level of neutralizing antibodies in pigs against two heterologous strains. A subsequent vaccination and challenge study in 48 pigs revealed that the chimeric virus VR2385-S3456 conferred an enhanced cross-protection when challenged with heterologous virus strain NADC20 or a contemporary heterologous strain RFLP 1-7-4. The results suggest that the chimera VR2385-S3456 may be a good PRRSV vaccine candidate for further development to confer heterologous protection.

Complete genomic sequence of an infectious pancreatic necrosis virus isolated from rainbow trout (Oncorhynchus mykiss) in China.

Infectious pancreatic necrosis (IPN) is a significant disease of farmed salmonids resulting in direct economic losses due to high mortality in China. However, no gene sequence of any Chinese infectious pancreatic necrosis virus (IPNV) isolates was available. In the study, moribund rainbow trout fry samples were collected during an outbreak of IPN in Yunnan province of southwest China in 2013. An IPNV was isolated and tentatively named ChRtm213. We determined the full genome sequence of the IPNV ChRtm213 and compared it with previously identified IPNV sequences worldwide. The sequences of different structural and non-structural protein genes were compared to those of other aquatic birnaviruses sequenced to date. The results indicated that the complete genome sequence of ChRtm213 strain contains a segment A (3099 nucleotides) coding a polyprotein VP2-VP4-VP3, and a segment B (2789 nucleotides) coding a RNA-dependent RNA polymerase VP1. The phylogenetic analyses showed that ChRtm213 strain fell within genogroup 1, serotype A9 (Jasper), having similarities of 96.3% (segment A) and 97.3% (segment B) with the IPNV strain AM98 from Japan. The results suggest that the Chinese IPNV isolate has relative closer relationship with Japanese IPNV strains. The sequence of ChRtm213 was the first gene sequence of IPNV isolates in China. This study provided a robust reference for diagnosis and/or control of IPNV prevalent in China.

Characterization of a Chikungunya virus strain isolated from banked patients' sera.

BackgroundChikungunya virus (CHIKV) is a prevalent mosquito-borne pathogen that is emerging in many parts of the globe causing significant human morbidity. Here, we report the isolation and characterization of an infectious CHIKV from banked serum specimens of suspected patients from the 2009 epidemic in Thailand.MethodsStandard plaque assay was used for CHIKV isolation from the banked serum specimens. Isolated CHIKV was identified base on E1 structural gene sequence. Growth kinetic, infectivity, cell viability and cytokine gene expression throughout CHIKV infection in a permissive cell line, 293T cells, was performed using several approaches, including standard plaque assay, immunofluorescence assay, classical MTT assay, and quantitative real-time PCR. Two tailed Student’s t test was used for evaluation statistically significance between the mean values of the groups.ResultsBased on the E1 structural gene sequence and phylogenetic analysis, we identified the virus as the CHIK/SBY8/10 isolate from Indonesia. Assessment of the growth kinetics, cytopathic effects as well as its ability to induce cellular immune responses suggested that the currently isolated CHIK/SBY8/10 virus is relatively more virulent than a known CHIKV vaccine strain, which also induces more dramatic proinflammatory responses.ConclusionsOur studies further add to the infectivity of a less-studied yet infectious CHIKV isolate as well as underscored the importance and utility of 293T cells as an excellent cell culture model for studying viral growth, CHIKV-induced inflammatory cellular responses and cell death. Together, these studies provide novel information on the CHIKV biology, infectivity and virus-cell interaction, which would help develop novel interventions against the infection.

Recharacterization of Morphological and Genetic Feature of Getah Virus Isolated from South Korea

Three QIAG93 strains, QIAG9301, QIAG9302 and QIAG9303 that have been identified as Getah virus (GETV) are analyzed in this study. The morphological features of three virus isolates were observed by using electron microscopy, suggesting that the QIAG9301, QIAG9302 and QIAG9303 isolate can be classified as tentative member of Alphavirus species in the Semliki Forest complex. The full length of the structural polyprotein gene of each QIAG93 isolate (QIAG9301, QIAG9302 and QIAG9303) was determined that are identical in size, comprising 3759 nucleotides that encoded 1253 amino acids. The sequence analysis of the structural polyprotein gene, including the C, E3, E1, 6K and E2 domain, showed that each QIAG93 isolate shares >98.9% sequence identity. The phylogenetic analysis and evolutionary distance (ED) estimation based on the structural polyprotein gene sequence showed that the QIAG9301 isolate is closely related to GETV South Korea strain (99.9% sequence identity and ED value 0.001) and Chinese GETV YN0540 strain (99.3% sequence identity ED value 0.007) than other Alphavirus species analyzed in this study. Both QIAG9032 and QIAG9303 isolate exhibited genetically close relationship with Mongolian GETV LEIV17741MPR strain (at least 99.3% sequence identity and mean ED value 0.0065). Therefore, our findings will be valuable for molecular epidemiological analyses of GETV in Korea and contribute to a further study on pathogenicity of three QIAG93 isolates in animals.

Antiplasmid Potential of <em>Kalanchoe blossfeldiana</em> Against Multidrug Resistance <em>Pseudomonas aeruginosa</em>

This study concerned with the isolation of Pseudomonas aeruginosa from various clinical cases in human which include (burn, wound and urine) that admitted to Emergency hospital and internal lab of teaching hospital in Erbil city. Forty isolates of P. aeruginosa from out of 120 samples were identified by using cultured, morphological and biochemical tests in addition to vitek machine. According to the resistance of the isolates to these antibiotics they showed variation in their resistance; the highest resistance was for penicillin G with 85% while the lowest resistance was for ceftizoxime with 40% and for others ranged between 42.5-82.5%. On the other hand the isolates P9, P16 and P30 were resist to all antibiotics under study. RCR was used to detect Exotoxin A (ETA) structural gene sequence. The result revealed that 82.5% of the isolates were positive for ETA gene. Methanolic and aqueous crude extract of Kalanchoe blossfeldiana were used as medicinal plant for curing agent for the reduction of antibiotic resistance genes of P. aeruginosa isolate P9, this was done through determination of Minimum Inhibitory Concentration (MIC) of this medicinal plant that used as curing agent which was 1800 µg/mL for aqueous extract and 1400 µg/mL for methanolic extract. The effect of MIC of methanolic extract on antibiotic resistance genes for isolate P9 showed reduction of the resistance from 44-100% while the effect of MIC of aqueous extract on antibiotic resistance genes for isolate P9 revealed decreasing of the resistance from 36-86%, respectively.

Phylogenetic relationships of Iranian Infectious Pancreatic Necrosis Virus (IPNV) based on deduced amino acid sequences of genome segment A and B cDNA

Infectious Pancreatic Necrosis Virus (IPNV) is the causal agent of a highly contagious disease that affects many species of fish and shellfish. This virus causes economically important diseases of farmed rainbow trout, Oncorhynchus mykiss, in Iran which is often associated with the transmission of pathogens from European resources. In this study, moribund rainbow trout fry were collected during an outbreak of IPNV in three different fish farms in one northern province (Mazandaran), and two west provinces (Chaharmahal and Bakhtiari, and Kohgiluyeh and Boyer Ahmad) of Iran. We investigated full genome sequence of Iranian IPNV and compared it with previously identified IPNV sequences. The sequences of different structural and non-structural protein genes were compared with other aquatic birnaviruses sequenced to date. Our results showed that the Iranian isolate fall within genogroup 5, serotype A2 strain SP, having 99 % identity with the strain 1146 from Spain. These results suggest that the Iranian isolate may have originated from Europe.

Sequence analysis of infectious pancreatic necrosis virus isolated from Iranian reared rainbow trout (Oncorhynchus mykiss) in 2012

Infectious pancreatic necrosis virus (IPNV) is the causal agent of a highly contagious disease that affects many species of fish and shellfish. This virus causes economically significant diseases of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), in Iran, which is often associated with the transmission of pathogens from European resources. In this study, moribund rainbow trout fry samples were collected during an outbreak of IPNV in three different fish farms in north and west provinces of Iran in 2012; and we investigated the full genome sequence of Iranian IPNV and compared it with previously identified IPNV sequences. The sequences of different structural and nonstructural-protein genes were compared to those of other aquatic birnaviruses sequenced to date. Our results show that the Iranian isolate falls within genogroup 5, serotype A2 strain SP, having 99% identity with the strain 1146 from Spain. These results suggest that the Iranian isolate may have originated from Europe.

Concurrent porcine circovirus type 2a (PCV2a) or PCV2b infection increases the rate of amino acid mutations of porcine reproductive and respiratory syndrome virus (PRRSV) during serial passages in pigs

Porcine reproductive and respiratory syndrome virus (PRRSV) has a high degree of genetic and antigenic variability. The purpose of this study was to determine if porcine circovirus type 2 (PCV2) infection increases genetic variability of PRRSV during serial passages in pigs and to determine if there is a difference in the PRRSV mutation rate between pigs concurrently infected with PCV2a or PCV2b. After 8 consecutive passages of PRRSV alone (group 1), PRRSV with PCV2a (group 2), or PCV2b (group 3) in pigs, the sequences of PRRSV structural genes for open reading frame (ORF) 5, ORF6, ORF7 and the partial non-structural protein gene (Nsp) 2 were determined. The total number of identified amino acid mutations in ORF5, ORF6, ORF7 and Nsp2 sequences was 30 for PRRSV infection only, 63 for PRRSV/PCV2a concurrent infection, and 77 for PRRSV/PCV2b concurrent infection when compared with the original VR2385 virus used to infect the passage 1 pigs. Compared to what occurred in pigs infected with PRRSV only, the mutation rates in ORF5 and ORF6 were significantly higher for concurrent PRRSV/PCV2b infected pigs. The PRRSV/PCV2a pigs had a significantly higher mutation rate in ORF7. The results from this study indicated that, besides ORF5 and Nsp2, the PRRSV structural genes ORF6 and ORF7 were shown to mutate at various degrees when the PRRSV was passaged over time in vivo. Furthermore, a significantly higher mutation rate of PRRSV was observed when pigs were co-infected with PCV2 highlighting the importance of concurrent infections on PRRSV evolution and control.

Detection of Exotoxin A gene in Pseudomonas aeruginosa from Clinical and Environmental samples

PCR was used to detect Pseudomonas aeruginosa from clinical and environmental samples by amplifying a 396-bp region of the exotoxin A (ETA) structural gene sequence. Specific primer amplified ETA – positive P. aeruginosa DNA, whereas other species of Pseudomonas and GC-rich bacteria did not yield any 396-bp fragment. The specificity of the assay was 1% (just one isolate from 100 isolates used in this study(,this gene is not present in these isolates which means that these isolates do not have the ability to produce the Exo A toxin. With this PCR method, ETA – positive P. aeruginosa was detected only in one water sample in comparison with the use of the 16SrDNA gene which yielded 100% positive results of all tested isolates. This PCR method is rapid and more accurate than other diagnostic methods for the identification of P. aeruginosa strains, and it can be used to detect a low level of P. aeruginosa from different samples without using a selective medium or additional biochemical tests.

Molecular cloning and characterization of GDP-mannose-3′,5′-epimerase from Gracilaria changii

GDP-mannose-3′,5′-epimerase (GME) is an enzyme involved in the biosynthesis of GDP-l-galactose which is a building unit of agar and cell wall polysaccharides. GME catalyzes the formation of GDP-β-l-galactose and GDP-l-gulose from GDP-mannose. In this study, the gene and transcript encoding GME from the red alga Gracilaria changii (GcGME) were cloned. The structural gene sequence of GcGME is devoid of an intron. The cis-acting regulatory element involved in light response is the most abundant element at the 5′-flanking region of GcGME. The open reading frame of GcGME consists of 1,053 nucleotides with 351 amino acids. This cDNA was cloned into pET32a expression vector for recombinant protein production in Escherichia coli. High yield of soluble recombinant GcGME (55 kDa) was expressed upon isopropyl β-d-1-thiogalactopyranoside induction. The enzyme activity of recombinant GcGME was detected using thin layer chromatography and high-performance liquid chromatography. The transcript abundance of GcGME was the highest in G. changii and the lowest in Gracilaria salicornia corresponding to their agar contents. The characterization of GcGME from G. changii is important to facilitate the understanding of its role in agar production of this seaweed.

Biomolecular Analyses of Starch and Starch Granule Proteins in the High-Amylose Rice Mutant Goami 2

Elevated proportions of amylose in cereals are commonly associated with either the loss of starch branching or starch synthase activity. Goami 2 is a high-amylose mutant of the temperate japonica rice variety Ilpumbyeo. Genotyping revealed that Goami 2 and Ilpumbyeo carry the same alleles for starch synthase IIa and granule-bound starch synthase I genes. Analyses of granule-bound proteins revealed that SSI and SSIIa accumulate inside the mature starch granules of Goami 2, which is similar to the amylose extender mutant IR36ae. However, unlike the amylose extender mutants, SBEIIb was still detectable inside the starch granules of Goami 2. Detection of SBEIIb after protein fractionation revealed that most of the SBEIIb in Goami 2 accumulates inside the starch granules, whereas most of it accumulates at the granule surface in Ilpumbyeo. Exhaustive mass spectrometric characterisations of granule-bound proteins failed to detect any peptide sequence mutation or major post-translational modifications in Goami 2. Moreover, the signal peptide was found to be cleaved normally from the precursor protein, and there is no apparent N-linked glycosylation. Finally, no difference was found in the SBEIIb structural gene sequence of Goami 2 compared with Ilpumbyeo. In contrast, a G-to-A mutation was detected in the SBEIIb gene of IR36ae located at the splice site between exon and intron 11, which could potentially introduce a premature stop codon and produce a truncated form of SBEIIb. It is suggested that the mutation responsible for producing high amylose in Goami 2 is not due to a defect in SBEIIb gene as was observed in IR36ae, even though it produces a phenotype analogous to the amylose extender mutation. Understanding the molecular genetic basis of this mutation will be important in identifying novel targets for increasing amylose and resistant starch contents in rice and other cereals.

A developmentally regulated lipocalin-like gene is overexpressed in Tomato yellow leaf curl virus-resistant tomato plants upon virus inoculation, and its silencing abolishes resistance

To discover genes involved in tomato resistance to Tomato yellow leaf curl virus (TYLCV), we previously compared cDNA libraries from susceptible (S) and resistant (R) tomato lines. Among the genes preferentially expressed in R plants and upregulated by TYLCV infection was a gene encoding a lipocalin-like protein. This gene was termed Solanum lycopersicum virus resistant/susceptible lipocalin (SlVRSLip). The SlVRSLip structural gene sequence of R and S plants was identical. SlVRSLip was expressed in leaves during a 15-day window starting about 40 days after sowing (20 days after planting). SlVRSLip was upregulated by Bemisia tabaci (the TYLCV vector) feeding on R plant leaves, and even more strongly upregulated following whitefly-mediated TYLCV inoculation. Silencing of SlVRSLip in R plants led to the collapse of resistance upon TYLCV inoculation and to a necrotic response along the stem and petioles accompanied by ROS production. Contrary to previously identified tomato lipocalin gene DQ222981, SlVRSLip was not regulated by cold, nor was it regulated by heat or salt. The expression of SlVRSLip was inhibited in R plants in which the hexose transporter gene LeHT1 was silenced. In contrast, the expression of LeHT1 was not inhibited in SlVRSLip-silenced R plants. Hence, in the hierarchy of the gene network conferring TYLCV resistance, SlVRSLip is downstream of LeHT1. Silencing of another gene involved in resistance, a Permease-I like protein, did not affect the expression of SlVRSLip and LeHT1; expression of the Permease was not affected by silencing SlVRSLip or LeHT1, suggesting that it does not belong to the same network. The triple co-silencing of SlVRSLip, LeHT1 and Permease provoked an immediate cessation of growth of R plants upon infection and the accumulation of large amounts of virus. SlVRSLip is the first lipocalin-like gene shown to be involved in resistance to a plant virus.