Analysis of sRNAs and Their mRNA Targets in Sinorhizobium meliloti: Focus on Half-Life Determination

Regulation of gene expression at the level of RNA and/or by regulatory RNA is an integral part of the regulatory circuits in all living cells. In bacteria, transcription and translation can be coupled, enabling regulation by transcriptional attenuation, a mechanism based on mutually exclusive structures in nascent mRNA. Transcriptional attenuation gives rise to small RNAs that are well suited to act in trans by either base pairing or ligand binding. Examples of 5'-UTR-derived sRNAs in the alpha-proteobacterium Sinorhizobium meliloti are the sRNA rnTrpL of the tryptophan attenuator and SAM-II riboswitch sRNAs. Analyses addressing RNA-based gene regulation often include measurements of steady-state levels and of half-lives of specific sRNAs and mRNAs. Using such measurements, recently we have shown that the tryptophan attenuator responds to translation inhibition by tetracycline and that SAM-II riboswitches stabilize RNA. Here we discuss our experience in using alternative RNA purification methods for analysis of sRNA and mRNA of S. meliloti. Additionally, we show that other translational inhibitors (besides tetracycline) also cause attenuation giving rise to the rnTrpL sRNA. Furthermore, we discuss the importance of considering RNA stability changes under different conditions and describe in detail a robust and fast method for mRNA half-life determination. The latter includes rifampicin treatment, RNA isolation using commercially available columns, and mRNA analysis by reverse transcription followed by quantitative PCR (RT-qPCR). The latter can be performed as a one-step procedure or in a strand-specific manner using the same commercial kit and a spike-in transcript as a reference.

A ParDE toxin-antitoxin system is responsible for the maintenance of the Yersinia virulence plasmid but not for type III secretion-associated growth inhibition

Many Gram-negative pathogens utilize the type III secretion system (T3SS) to translocate virulence-promoting effector proteins into eukaryotic host cells. The activity of this system results in a severe reduction of bacterial growth and division, summarized as secretion-associated growth inhibition (SAGI). In Yersinia enterocolitica, the T3SS and related proteins are encoded on a virulence plasmid. We identified a ParDE-like toxin-antitoxin system on this virulence plasmid in genetic proximity to yopE, encoding a T3SS effector. Effectors are strongly upregulated upon activation of the T3SS, indicating a potential role of the ParDE system in the SAGI or maintenance of the virulence plasmid. Expression of the toxin ParE in trans resulted in reduced growth and elongated bacteria, highly reminiscent of the SAGI. Nevertheless, the activity of ParDE is not causal for the SAGI. T3SS activation did not influence ParDE activity; conversely, ParDE had no impact on T3SS assembly or activity itself. However, we found that ParDE ensures the presence of the T3SS across bacterial populations by reducing the loss of the virulence plasmid, especially under conditions relevant to infection. Despite this effect, a subset of bacteria lost the virulence plasmid and regained the ability to divide under secreting conditions, facilitating the possible emergence of T3SS-negative bacteria in late acute and persistent infections.

Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics

The soil-dwelling plant symbiont Sinorhizobium meliloti is a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, identification of translated sORFs is critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) can detect translated sORFs with high sensitivity, but is not yet routinely applied to bacteria because it must be adapted for each species. Here, we established a Ribo-seq procedure for S. meliloti 2011 based on RNase I digestion and detected translation for 60% of the annotated coding sequences during growth in minimal medium. Using ORF prediction tools based on Ribo-seq data, subsequent filtering, and manual curation, the translation of 37 non-annotated sORFs with ≤ 70 amino acids was predicted with confidence. The Ribo-seq data were supplemented by mass spectrometry (MS) analyses from three sample preparation approaches and two integrated proteogenomic search database (iPtgxDB) types. Searches against standard and 20-fold smaller Ribo-seq data-informed custom iPtgxDBs confirmed 47 annotated SEPs and identified 11 additional novel SEPs. Epitope tagging and Western blot analysis confirmed the translation of 15 out of 20 SEPs selected from the translatome map. Overall, by combining MS and Ribo-seq approaches, the small proteome of S. meliloti was substantially expanded by 48 novel SEPs. Several of them are part of predicted operons and/or are conserved from Rhizobiaceae to Bacteria, suggesting important physiological functions.

Incoherent dual regulation by a SAM-II riboswitch controlling translation at a distance

In Sinorhizobium meliloti, the methionine biosynthesis genes metA and metZ are preceded by S-adenosyl-L-methionine (SAM) riboswitches of the SAM-II class. Upon SAM binding, structural changes in the metZ riboswitch were predicted to cause transcriptional termination, generating the sRNA RZ. By contrast, the metA riboswitch was predicted to regulate translation from an AUG1 codon. However, downstream of the metA riboswitch, we found a putative Rho-independent terminator and an in-frame AUG2 codon, which may contribute to metA regulation. We validated the terminator between AUG1 and AUG2, which generates the sRNA RA1 that is processed to RA2. Under high SAM conditions, the activities of the metA and metZ promoters and the steady-state levels of the read-through metA and metZ mRNAs were decreased, while the levels of the RZ and RA2 sRNAs were increased. Under these conditions, the sRNAs and the mRNAs were stabilized. Reporter fusion experiments revealed that the Shine–Dalgarno (SD) sequence in the metA riboswitch is required for translation, which, however, starts 74 nucleotides downstream at AUG2, suggesting a novel translation initiation mechanism. Further, the reporter fusion data supported the following model of RNA-based regulation: Upon SAM binding by the riboswitch, the SD sequence is sequestered to downregulate metA translation, while the mRNA is stabilized. Thus, the SAM-II riboswitches fulfil incoherent, dual regulation, which probably serves to ensure basal metA and metZ mRNA levels under high SAM conditions. This probably helps to adapt to changing conditions and maintain SAM homoeostasis.

Structural and functional conservation of cis-acting RNA elements in coronavirus 5'-terminal genome regions

Structure predictions suggest a partial conservation of RNA structure elements in coronavirus terminal genome regions. Here, we determined the structures of stem-loops (SL) 1 and 2 of two alphacoronaviruses, human coronavirus (HCoV) 229E and NL63, by RNA structure probing and studied the functional relevance of these putative cis-acting elements. HCoV-229E SL1 and SL2 mutants generated by reverse genetics were used to study the effects on viral replication of single-nucleotide substitutions predicted to destabilize the SL1 and SL2 structures. The data provide conclusive evidence for the critical role of SL1 and SL2 in HCoV-229E replication and, in some cases, revealed parallels with previously characterized betacoronavirus SL1 and SL2 elements. Also, we were able to rescue viable HCoV-229E mutants carrying replacements of SL2 with equivalent betacoronavirus structural elements. The data obtained in this study reveal a remarkable degree of structural and functional conservation of 5′-terminal RNA structural elements across coronavirus genus boundaries.

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Conservation of 5'-terminal SL1 and SL2 elements in alpha- and betacoronaviruses.

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HCoV-229E reverse genetics data suggest critical role for SL1/2 in viral replication.

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Replacement of SL2 in HCoV-229E with betacoronavirus equivalents is tolerated.

Abstract OT3-07-03: Positive behavior change and weight loss in breast cancer survivors on hormonal adjuvant therapy: An energy balance research in cancer (EnBaR) prospective study

BACKGROUND: Observational studies have repeatedly linked obesity to increased cancer incidence, recurrence, and mortality, leading to cancer treatment guidelines that call for maintenance of a healthy body weight, regular physical activity (PA) regardless of body mass index (BMI), and modest weight loss for overweight and obese cancer survivors (CS). Despite these recommendations, newly published reports suggest that more than 70% of CS are overweight or obese, and only 1/3 engage in the recommended levels of PA. Although trials have demonstrated that energy balance (EB) interventions are feasible in CS, it has been concluded that ongoing behavioral support is needed to implement and sustain changes in weight and PA. Through the subsequent Energy Balance Research (EnBaR) the incorporation of a weight management and PA program focused on ongoing behavioral support for breast cancer survivors (BCS) as an effective method for implementation of lifestyle modifications will be investigated.

TRIAL DESIGN: This is a single-arm prospective observational study investigating if implementation of an EB Program for BCS is an effective intervention for producing lifestyle behaviors. Eligible subjects must be female BCS ≥18 years with BMI ≥25 who are initiating hormonotherapy (HT) as their only oncology treatment modality. Subjects will consult with a Registered Dietitian (RD) to establish goals based on specified interventions for reducing overall BMI at the time of initiating their prescribed HT. Subjects will subsequently receive telephone calls from the RD at bi-monthly intervals to discuss the established points of intervention, answering questions proposed by the RD from a set intervention measurement scale. Patients will also report for body composition analysis performed by the RD via InBody at Baseline, Day 90, and Day 180. InBody is a validated tool that utilizes direct segmental multi-frequency bioelectrical impedance analysis (DSM-BIA) to provide a highly accurate report of an individual's body composition.

AIMS: Determine change in Percent Body Fat (PBF) and BMI during adjuvant hormone treatment for breast cancer patients.

STATS/TARGET ACCRUAL: To assess % change in BMI and PBF between baseline and 180 days, one-sample t-tests will be used. Assuming an average (avg) baseline BMI of 33.7 with a standard deviation of 8.5; a sample of 120 patients will yield 89.4% power using a two-sided t-test to detect a 13% reduction in BMI to an avg of 29.32 and 82.8% power to detect a 12% reduction to an avg BMI of 29.656. Similarly, a t-test will have 83.7% power to detect a 12% decrease in % change in PBF assuming an avg baseline PBF of 41.36 with a standard deviation 10.5. The power calculations were accomplished by generating simulations of size 10,000 replications conducted at the 0.025 significance level using the TTEST procedure of SAS 9.4 [SAS Institute Inc., Cary, NC, USA]. The calculations assume a linear correlation of 0.5 between the baseline and Day 180 measurements and are Bonferroni corrected to maintain a familywise error of 0.05 for the primary analysis. All statistical analyses will be conducted using SAS 9.4. Statistical significance will be defined as p < 0.05.

Citation Format: Scheuer R, Bendinger GM, Ensor Jr. JE, Nixon D, Randolph K, McGuirec E, Rados K, McNight JE, Pabbathi H, Panicker R, Johnson AT, Langlois C, Lammersfeld C, Alvarez RH. Positive behavior change and weight loss in breast cancer survivors on hormonal adjuvant therapy: An energy balance research in cancer (EnBaR) prospective study [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT3-07-03.

Comparison of ELISA and HPLC for the determination of histamine in cheese

A competitive direct enzyme-linked immunosorbent assay (CD-ELISA) for histamine in cheese was compared with a reversed-phase liquid chromatography (RP-HPLC) method. Cheese was homogenized with phosphate-buffered saline (PBS), centrifuged, and filtered, and the supernatant was diluted with PBS for CD-ELISA. For RP-HPLC, biogenic amines (histamine, tyramine, putrescine, and cadaverine) were derivatized with 9-fluorenylmethylchloroformate, followed by reversed-phase chromatography and fluorescence detection. Detection limits and mean recoveries (10-1000 mg/kg) were 2 mg/kg and 93% for CD-ELISA and 1 mg/kg and 99% for RP-HPLC, respectively. Analysis of 50 commercial cheeses according to both methods showed good agreement for histamine (r = 0.979; concentration range = 2-1800 mg/kg). At a threshold level of 10 mg/kg, the ELISA gave no false-negative and three false-positive results. The results show that the ELISA is suitable for the determination of histamine in cheese.

Assessment of soluble adhesion molecules (sICAM-1, sVCAM-1, sELAM-1) and complement cleavage products (sC4d, sC5b-9) in urine. Clinical monitoring of renal allograft recipients

Increasing evidence exists that inducible adhesion molecules are involved in cell-mediated allograft rejection. In addition, complement activation during rejection has been described. This study investigated, whether specific molecules derived from either pathway are excreted into urine during rejection and whether they can provide useful diagnostic tools for the monitoring of renal transplant recipients. Urinary concentrations of soluble adhesion molecules (sICAM-1, sVCAM-1, sE-selectin) and of complement cleavage products (sC4d and sC5b-9), were determined by standardized ELISA in 30 normal controls and 80 samples from 49 recipients of renal allografts. In contrast to the low amounts of adhesion molecules and complement components uniformly excreted by healthy persons (group 0), marked differences were observed among allograft recipients. To prove the clinical relevance of these differences in excretion, patient samples were assigned to 5 categories according to clinical and histopathological criteria: group I--acute steroid-resistant rejection (n = 10); group II--acute steroid-sensitive rejection (n = 10); group III--chronic rejection (n = 23); group IV--stable graft function (n = 27); and group V--miscellaneous disorders (n = 10), including infections, CsA overdoses, and glomerulonephritis. Urinary levels of sICAM-1, sVCAM-1, and sC4d were significantly higher in group I compared with all other groups (P < 0.01). The difference in sICAM-1 excretion between groups III and IV also reached statistical significance (P < 0.05). Urinary concentrations of sICAM-1, sVCAM-1, and sC4d were reflective of their histological distribution in corresponding graft biopsies. None of the patients excreted E-selectin in detectable amounts. Excretion of the terminal membrane attack complex C5b-9 was not significantly associated with any diagnosis. It is concluded that for clinical purposes the combined evaluation of sICAM-1, sVCAM-1, and sC4d is most useful and can provide valuable information with regard to the severity and the type of allograft rejection.

Diabetic neuropathy 3 years after successful pancreas and kidney transplantation

Twenty-seven patients with successful transplantation and a control group of 14 patients with early rejection of the pancreas graft but functioning kidney graft were examined in a prospective study for 3 yr. Before transplantation, all patients had long-standing type I diabetes with advanced secondary complications, including end-stage diabetic nephropathy. After transplantation in the patients of both groups, kidney function was almost normal. Mean HbA1 levels were normal in the group with pancreas graft survival. In the control group, HbA1 levels were, on average, 1.5% higher compared with the group with pancreas survival (P = 0.00005). After 3 yr, the patients with functioning pancreas graft showed fewer symptoms (mean difference 1.0 in a symptom score ranging from 0 to 16, P = 0.004) compared with the control group. No statistically significant difference between both groups concerning clinical signs of polyneuropathy could be observed. In the pancreas and kidney transplantation group, peroneal and median nerve conduction velocities increased 7.2 m/s (P < 0.01) and 3.5 m/s (P < 0.05), respectively, whereas no increase was registered in the control group. The change of median and sural sensory nerve conduction velocities, peroneal and median compound muscle action potentials, and sural and median sensory action potentials was insignificant. In conclusion, although the improvement of clinical symptoms and neurophysiological signs of polyneuropathy was modest in the pancreas and kidney transplantation group, our data suggest that successful pancreas transplantation is able not only to halt the progression of diabetic polyneuropathy but also to improve it to some extent even at a far advanced stage.

Research in the hospital setting on human subjects. Protecting the patient and the institution

A hospital's institutional review board is charged with the responsibility of fully protecting the rights of research subjects. In doing so, the board establishes that research protocols are based on sound scientific principles, that benefits to research subjects outweigh the risks, and that the subject's consent is informed and not coerced. Although it has been argued that risk management has no role in the activities of such boards, the literature indicates that risk management and quality assurance principles apply to all areas of the institution, including the activities of the board. The institution must ensure that its researchers and board members are as fully protected as possible from civil and criminal liability and that the integrity of those conducting the research is established and maintained. The institution must also provide sufficient support for the board to conduct its reviews and educate the research community and board members on current and evolving laws and regulations governing human research. Risk prevention and quality assurance strategies should recognize the rights of the research subject as paramount while protecting the institution, its researchers, and the community served.

High incidence of carpal tunnel syndrome in diabetic patients after combined pancreas and kidney transplantation

Fifty-eight patients with long-standing type 1 (insulin-dependent) diabetes were studied prospectively after combined pancreas and kidney transplantation for a mean observation period of 47.9 months (range 17-116 months). Thirty-three per cent of these patients (19/58) developed carpal tunnel syndrome after a mean interval of 1.7 years (range 3 months-5 years). This rate is about twice that in type 1 diabetic patients. The manifestation of carpal tunnel syndrome was not significantly associated with worsening of diabetic polyneuropathy or with deterioration of kidney or pancreas function. In all but one patient symptoms improved without surgical intervention. This study suggests that patients after combined pancreas and kidney transplantation have an increased risk of carpal tunnel syndrome for which the etiology and pathophysiology are unknown. In most patients no surgical intervention is necessary.

Effect of pancreatic and/or renal transplantation on diabetic autonomic neuropathy

Thirty-nine Type 1 (insulin-dependent) diabetic patients were studied prospectively after simultaneous pancreas and kidney (n = 26) and kidney grafting alone (n = 13) by measuring heart rate variation during various maneuvers and answering a standardized questionnaire every 6 to 12 months post-transplant. While age, duration of diabetes, and serum creatinine (168.1 +/- 35.4 vs 132.7 +/- 17.7 mumol/l) were comparable, haemoglobin A1 levels were significantly lower (6.6 +/- 0.2 vs 8.5 +/- 0.3%; p less than 0.01) and the mean observation time longer (35 +/- 2 vs 25 +/- 3 months; p less than 0.05) in the pancreas recipients when compared with kidney transplanted patients. Heart rate variation during deep breathing, lying/standing and Valsalva manoeuver were very similar in both groups initially and did not improve during follow-up. However, there was a significant reduction in heart rate in the pancreas recipient group. Autonomic symptoms of the gastrointestinal and thermoregulatory system improved more in the pancreas grafted subjects, while hypoglycaemia unawareness deteriorated in the kidney recipients. This study suggests that long-term normoglycaemia by successful pancreatic grafting is able to halt the progression of autonomic dysfunction.

Metabolic control and effect on secondary complications of diabetes mellitus by pancreatic transplantation

After successful pancreatic transplantation blood glucose can be normalized without exogenous insulin, although oral and intravenous glucose tolerance remains impaired in 10-45% of the patients. There is no significant deterioration of glucose control with time in most patients. Since most recipients of pancreatic grafts have far advanced secondary diabetic lesions and the observation time after grafting is rather short, the effects of pancreatic transplantation on these complications are difficult to interpret. However, the development of diabetic nephropathy can be prevented, skin microcirculation improves significantly, while autonomic and peripheral neuropathy and diabetic retinopathy remain stable or improve slightly in most patients. But these ameliorations may be in part due to elimination of uraemia, since in almost all patients combined pancreas/kidney transplantations were performed. It is concluded that pancreas grafting probably has to be performed much earlier in the course of diabetes, although the improvement in the quality of life is striking even in the end-stage diabetics studied so far.