A genomics-led approach to deciphering the mechanism of thiotetronate antibiotic biosynthesis

Thiolactomycin (TLM) is a thiotetronate antibiotic that selectively targets bacterial fatty acid biosynthesis through inhibition of the β-ketoacyl-acyl carrier protein synthases (KASI/II) that catalyse chain elongation on the type II (dissociated) fatty acid synthase. It has proved effective in in vivo infection models of Mycobacterium tuberculosis and continues to attract interest as a template for drug discovery. We have used a comparative genomics approach to uncover the (hitherto elusive) biosynthetic pathway to TLM and related thiotetronates. Analysis of the whole-genome sequence of Streptomyces olivaceus Tü 3010 producing the more ramified thiotetronate Tü 3010 provided initial evidence that such thiotetronates are assembled by a novel iterative polyketide synthase-nonribosomal peptide synthetase, and revealed the identity of other pathway enzymes, encoded by adjacent genes. Subsequent genome sequencing of three other thiotetronate-producing actinomycetes, including the Lentzea sp. ATCC 31319 that produces TLM, confirmed that near-identical clusters were also present in these genomes. In-frame gene deletion within the cluster for Tü 3010 from Streptomyces thiolactonus NRRL 15439, or within the TLM cluster, led to loss of production of the respective thiotetronate, confirming their identity. Each cluster houses at least one gene encoding a KASI/II enzyme, suggesting plausible mechanisms for self-resistance. A separate genetic locus encodes a cysteine desulfurase and a (thiouridylase-like) sulfur transferase to supply the sulfur atom for thiotetronate ring formation. Transfer of the main Tü 3010 gene cluster (stu gene cluster) into Streptomyces avermitilis led to heterologous production of this thiotetronate, showing that an equivalent sulfur donor can be supplied by this host strain. Mutational analysis of the Tü 3010 and TLM clusters has revealed the unexpected role of a cytochrome P450 enzyme in thiotetronate ring formation. These insights have allowed us to propose a mechanism for sulfur insertion, and have opened the way to engineering of the biosynthesis of TLM and other thiotetronates to produce novel analogues.

Identification and characterisation of tobacco microRNA transcriptome using high-throughput sequencing

MicroRNAs (miRNAs) are post-transcriptional regulators that are involved in numerous biological processes in plants. In this study, we investigate miRNAs in Honghua Dajinyuan, an agronomically important species of tobacco in China. Here, we report a comprehensive analysis of miRNA expression profiles in the leaf, stem and root using a high-throughput sequencing approach. A total of 165 miRNAs, representing 55 conserved families, and 50 novel miRNAs, representing 19 families, were identified in three libraries. In addition, 12 miRNAs were randomly selected from a differentially expressed conserved miRNA family in three libraries with expression alterations and subjected to qRT-PCR validation. Of these, the expression level of nta-miR167d is highly enriched in the leaf tissue. In addition, the expression level of nta-miR319a is prominently enriched in the stem, while nta-miR160c is highly enriched in the root. Moreover, the target prediction showed that most of the targets coded for transcription factors that are involved in cellular and metabolic processes. GO analysis showed that most of the targets were involved in organelle function, served binding functions, and take part in cellular and metabolic processes. This study helps shed new light on understanding the role of miRNAs in different parts of the tobacco plant and adds a significant number of novel miRNAs to the tobacco miRNA transcriptome.

Visualization of the Peripheral Branches of the Mandibular Division of the Trigeminal Nerve on 3D Double-Echo Steady-State with Water Excitation Sequence

BACKGROUND AND PURPOSE

Although visualization of the extracranial branches of the cranial nerves has improved with advances in MR imaging, only limited studies have assessed the detection of extracranial branches of the mandibular nerve (V3). We investigated the detectability of the branches of V3 on a 3D double-echo steady-state with water excitation sequence.

MATERIALS AND METHODS

We retrospectively evaluated the detectability of the 6 branches of the V3, the masseteric, buccal, auriculotemporal, lingual, inferior alveolar, and mylohyoid nerves, by using a 5-point scale (4, excellent; 3, good; 2, fair; 1, poor; and 0, none) in 86 consecutive patients who underwent MR imaging with the 3D double-echo steady-state with water excitation sequence. Weighted κ analysis was used to calculate interobserver variability among the 3 readers.

RESULTS

The detection of the lingual and inferior alveolar nerves was the most successful, with excellent average scores of 3.80 and 3.99, respectively. The detection of the masseteric, the buccal, and the auriculotemporal nerves was good, with average scores of 3.31, 2.67, and 3.11, respectively. The mylohyoid nerve was difficult to detect with poor average scores of 0.62. All nerves had excellent interobserver variability across the 3 readers (average weighted κ value, 0.95-1.00).

CONCLUSIONS

The 3D double-echo steady-state with water excitation sequence demonstrated excellent visualization of the extracranial branches of V3 in most patients. The 3D double-echo steady-state with water excitation sequence has the potential for diagnosing V3 pathologies and preoperatively identifying peripheral cranial nerves to prevent surgical complications.

Evaluation of normal changes in pons metabolites due to aging using turbo spectroscopic imaging

BACKGROUND AND PURPOSE

To date, MRS study of both normal and pathologic brains have focused mainly on the supratentorial regions; few studies have investigated the infratentorial regions. However, the pons, an important structure of the brain, is associated with many neurodegenerative diseases and is often damaged by brain trauma. For MRS study of pontine disease, one must obtain MRS reference data on normal metabolite levels in the pons, including data on how these levels vary with age. The aim of this study was to analyze normal, age-related, metabolic changes in the pons by using turbo spectroscopic imaging.

MATERIALS AND METHODS

Seventy-eight healthy subjects with ages ranging from 5 days to 78 years were included in this study. NAA/Cr, Cho/Cr, and Cho/NAA ratios were measured by using turbo spectroscopic imaging. The 78 cases were divided into 4 groups by age: 0-5, 6-20, 21-50, and older than 50 years. The metabolite levels were compared with observed age-related changes among the groups.

RESULTS

The normal mean pontine metabolite ratios obtained for the combined age groups were NAA/Cr, 2.44 ± 0.45 (mean); Cho/Cr, 1.93 ± 0.25; and Cho/NAA, 0.83 ± 0.28. Statistically significant differences were found in the NAA/Cr between the 0- to 5- and 6- to 20-year-old groups, and among the 6- to 20-, 21- to 50-, and older than 50-year-old groups. A statistically significant difference was found in Cho/Cr between the 0- to 5- and 6- to 20-year-old subjects; however, no differences were found among the 6- to 20-, 21- to 50-, and older than 50-year-old groups. Statistically significant differences in Cho/NAA were also found among the 4 age groups. The NAA/Cr at birth was low, it rose rapidly at 0-5 years, reaching a peak at approximately 10-20 years, and then gradually decreased. The Cho/Cr decreased rapidly at 0-5 years, then continued to decline, and was stable after 20 years of age.

CONCLUSIONS

Turbo spectroscopic imaging is a good method for analyzing normal changes in the pons metabolites during growth, maturation, and aging.

Note: Design and initial results of a multi-pulsed intense electron beam source

A multi-pulsed intense electron beam source is introduced, including the design and the initial experimental results. The source can generate a burst of three pulses of intense electron beams with energy of 2-3 MeV and beam intensities of around 2.5 kA. An inductive adder is chosen to generate the pulsed diode voltages and a dispenser cathode is chosen to emit electron beams. The test results indicate that the design of the source is reliable. The multi-pulsed diode voltage is up to 2.5 MV and the beam intensities are more than 2 kA at the exit of the source with small variation.

Reovirus-associated meningoencephalomyelitis in baboons

Baboon orthoreovirus (BRV) is associated with meningoencephalomyelitis (MEM) among captive baboons. Sporadic cases of suspected BRV-induced MEM have been observed at Southwest National Primate Research Center (SNPRC) for the past 20 years but could not be confirmed due to lack of diagnostic assays. An immunohistochemistry (IHC)-based assay using an antibody against BRV fusion-associated small transmembrane protein p15 and a conventional polymerase chain reaction (PCR)-based assay using primers specific for BRV were developed to detect BRV in archived tissues. Sixty-eight cases of suspected BRV-induced MEM from 1989 through 2010 were tested for BRV, alphavirus, and flavivirus by IHC. Fifty-nine of 68 cases (87%) were positive for BRV by immunohistochemistry; 1 tested positive for flavivirus (but was negative for West Nile virus and St Louis encephalitis virus by real-time PCR), and 1 virus isolation (VI) positive control tested negative for BRV. Sixteen cases (9 BRV-negative and 7 BRV-positive cases, by IHC), along with VI-positive and VI-negative controls, were tested by PCR for BRV. Three (of 9) IHC-negative cases tested positive, and 3 (of 7) IHC-positive cases tested negative by PCR for BRV. Both IHC and PCR assays tested 1 VI-positive control as negative (sensitivity: 75%). This study shows that most cases of viral MEM among baboons at SNPRC are associated with BRV infection, and the BRV should be considered a differential diagnosis for nonsuppurative MEM in baboons.

Effect of vitamin E supplementation on α-tocopherol and β-carotene concentrations in tissues from pasture- and grain-fed cattle

The effects of dietary vitamin E supplementation of grain-fed cattle on lipid oxidation and meat colour have been extensively investigated, but little attention has been given to pasture-fed cattle where meat is likely to contain naturally high amounts of α-tocopherol and carotenoids. In the work described, we evaluated the effects of pasture-feeding alone and with vitamin E supplementation on tissue levels of anti-oxidants and compared the findings with those obtained for grain-fed cattle with and without supplementation. Sorghum was the major component of the grained-based ration. α-Tocopherol concentrations in plasma, muscle and fat tissues of pasture-fed cattle were not affected by vitamin E supplementation (2500 IU/head/day for 132 days prior to slaughter) while those of grain-fed cattle increased significantly. The α-tocopherol concentrations in the supplemented grain-fed cattle were similar in muscle and liver to pasture-fed animals but were lower in their fat (P<0.05). The major carotenoid present in all tissues studied from pasture-fed was β-carotene and its contents in plasma, liver, fat and muscles were decreased (P<0.05) by supplementation with vitamin E. Carotenoids were essentially absent in grain-fed cattle except for small amounts in liver. The implication of this study for the meat industry is that cattle grazed on good pasture can achieve concentrations of α-tocopherol in muscles and other tissues at least as high as those obtained by supra-nutritional supplementation of grain-fed cattle with vitamin E. However, α-tocopherol supplementation of pasture-fed cattle reduced tissue concentrations of β-carotene, which would reduce carcase fat yellowness and make pasture-fed cattle more acceptable to some Asian markets.

Lipid stability and meat colour of beef from pasture- and grain-fed cattle with or without vitamin E supplement

Meat from pasture-fed cattle can have high contents of α-tocopherol and other anti-oxidants originating from naturally occurring compounds present in grasses. However, meat from pasture-fed cattle may have an increased demand for endogenous anti-oxidants because of its high content of polyunsaturated fatty acids, which in turn, may affect its colour and lipid stability. In the work described, we evaluated the effects of pasture-feeding alone and with vitamin E supplementation and compared the findings with those obtained for grain-fed cattle (predominantly sorghum) with and without supplementation. Within each nutritional background, vitamin E supplementation did not alter meat colour or colour stability of fresh or 47-day aged muscle during 7-day aerobic storage. However, both control and supplemented grain-fed product had better meat colour (more redness) compared with meat from grass-fed cattle. These differences in redness between pasture- and grain-fed fresh beef were not apparent after ageing. The treatments did not affect the lipid stability of fresh meat during aerobic storage; however, supplementation reduced (P<0.01) lipid oxidation in grain-fed aged beef compared with pasture-fed aged beef, despite both having similar α-tocopherol contents. Pasture-fed beef had more linolenic acid, less linoleic acid and, overall, was more polyunsaturated than grain-fed beef (P<0.05). In summary, vitamin E supplementation of pasture-fed cattle did not alter muscle tocopherol contents but pasture-fed beef (both control and supplemented) was more susceptible to lipid oxidation following ageing than vitamin E supplemented grain-fed beef.

A comparison of fat composition of Japanese and long-term grain-fed Australian steers

Subcutaneous and intermuscular fat samples were collected from carcases of four major breeds of steers in Japan: Wagyu, Wagyu × Angus, Dairy and Murray Grey. For comparison, we also collected subcutaneous fat samples from carcases of long-term grain-fed (350-455 days) Angus, Jersey and Angus × Hereford steers, and short-term grain-fed (70-100 days) Murray Grey steers in Australia. Fatty acid profiles were determined on all samples and triacylglycerol composition, thermal properties, fat cell size and lipid and connective tissue contents were determined on representative samples. Compared with the Japanese samples which were soft to very soft when assessed subjectively, samples of Australian fat were generally hard and somewhat fibrous in appearance. These tactile and visual differences in the hardness of the subcutaneous fat between the Japanese and Australian beef were confirmed by the physical and chemical properties determined. Markedly different melting patterns were observed for the Australian and Japanese fat samples. The Japanese fat had considerably less saturated and more unsaturated fatty acids resulting in much higher unsaturated/saturated ratios (1.9) compared with the Australian samples (1.0). This resulted primarily from the high contents of oleic and palmitoleic acids and the low content of stearic acid of the Japanese samples. The triacylglycerols from the Japanese fat had considerably less tri-saturated and di-saturated fatty acids and more di-monounsaturated and tri-monounsaturated fatty acids in their structure. Differences were observed when the Japanese subcutaneous fat samples were grouped by their meat quality grades. From Grade 5 to Grade 2, there was a significant decrease in marbling score (9.3 to 2.5) and in the ratio of palmitoleic to stearic acid (1.7 to 1.2) and an increase in the connective tissue content (1.5 to 2.1%). Compared with subcutaneous fat, intermuscular fat had a higher content of saturated and a lower content of unsaturated fatty acids resulting in a lower ratio of unsaturated to saturated fatty acids and of palmitoleic to stearic acid. It was concluded that the fatty acid composition and the triacylglycerol structure of fat plays the predominant role in determining the lustre, texture and properties of fat desired by the Japanese market: the soft character of fat from Japanese cattle results primarily from its low content of stearic acid and consequent lower melting temperatures. Fat cell size and the lipid and connective tissue contents of fat appear to be less important.