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Background: Enhanced recovery pathways (ERPs) aim to lower perioperative stress to facilitate recovery. Limited fasting combined with carbohydrate loading is a common ERP element. The effect of limited fasting has not been elucidated in patients with diabetes. Given the known deleterious effects of poor glycemic control in the perioperative period, such as increased rates of surgical site infection, the associations of preoperative limited fasting with perioperative glycemic control and early outcomes after lower extremity bypass (LEB) were investigated., Methods: A single institutional retrospective review of patients who underwent infrainguinal LEB from 2016 to 2022 was performed. The ERP was initiated in May 2018. Patients were stratified by diabetes diagnosis and preoperative hemoglobin A1C (HbA1C) levels. Perioperative glycemic control was compared between the limited fasting and traditional fasting patients (nil per os at midnight). Limited fasting was defined as a clear liquid diet until 2 hours before surgery with recommended carbohydrate loading consisting of 400 cc of a clear sports drink (approximately 30 g of carbohydrates). All limited fasting patients were within the ERP. Early perioperative hyperglycemia (EPH) was defined as blood glucose of >180 mg/dL within the first 24 hours of surgery. Perioperative outcomes such as surgical site infection, readmission, reinterventions, and complications were also compared., Results: A total of 393 patients were included (limited fasting patients N = 135; traditional fasting patients N = 258). A trend toward EPH was seen in all limited fasting groups. Evaluating limited fasting within diabetic patients revealed that 74.5% of limited fasting-diabetic patients had EPH compared with 49.6% of traditional fasting-diabetic patients (P = .001). When stratified by the HbA1C level, a significantly higher rate of EPH was seen in the HbA1c >8.0% groups, with 90.5% in the limited fasting patients compared with 67.9% in traditional fasting patients (P = .05). Limited fasting-diabetic patients experience a longer postoperative length of stay at 5.0 days (interquartile range: 3, 9) vs 4.0 days (2, 6) in nondiabetic patients (P = .016)., Conclusions: ERP limited fasting was associated with early perioperative hyperglycemia after LEB, particularly in patients with HbA1C >8.0%. Due to the high prevalence of diabetic patients undergoing LEB under ERP, the role of limited fasting and common glycemic elements of ERP may need to be re-evaluated in this subpopulation., (Published by Elsevier Inc.)

Background: Anatomic remodeling within the thoracic aorta following thoracic endovascular aortic repair (TEVAR) for type B aortic dissection (TBAD) has been well documented. However, less is known about the response of the untreated visceral aorta. In the present study, we investigated the visceral aortic behavior after TEVAR for acute or subacute TBAD to identify any associations with the clinical outcomes., Methods: A multicenter retrospective review was performed of all imaging studies for all patients who had undergone TEVAR for acute (0-14 days) and subacute (14-90 days) nontraumatic TBAD from 2006 to 2020. The cohort was inclusive of those with uncomplicated, high-risk, and complicated (defined in accordance with the Society for Vascular Surgery reporting guidelines) dissections. Centerline aortic measurements of the true and false lumen and total aortic diameter (TAD) were taken at standardized locations relative to the aortic anatomy within each aortic zone (the zones were defined by the Society for Vascular Surgery reporting guidelines). Diameter changes over time were evaluated using repeated measures mixed effects linear growth modeling. Visceral segment instability (VSI) was defined as any growth in the TAD of ≥5 mm within aortic zones 5 through 9., Results: A total of 82 patients were identified. The median length of imaging follow-up was 2.1 years (interquartile range, 0.75-4.5 years), with 15% of the cohort having follow-up >5 years. VSI was present in 55% of the cohort, with an average maximal increase in the TAD of 10.4 ± 6.3 mm during a median follow-up of 2.1 years (interquartile range, 0.75-4.5 years). Approximately one third of the cohort had experienced rapid VSI (growth ≥5 mm in the first year), and 4.8% of the cohort had developed a large paravisceral aortic aneurysm (TAD ≥5 cm) secondary to VSI. Linear growth modeling identified significant predictable growth in the TAD across all visceral zones. Zone 7 had the highest rate of TAD dilation, with a fixed effect estimated rate of 1.3 mm/y (95% confidence interval [CI], 0.23-2.1; P = .022). The preoperative factor most strongly associated with VSI was a cumulative number of zones dissected of six or more (odds ratio, 6.4; 95% CI, 1.07-8.6; P = .041). The odds for aortic reintervention were significantly increased for cases in which VSI led to the development of a paravisceral aortic aneurysm of ≥5 cm (odds ratio, 3.7; 95% CI, 1.1-13; P = .038)., Conclusions: VSI was identified in most patients who had undergone TEVAR for management of acute and subacute TBAD. The preoperative anatomic features such as the dissection extent, rather than the procedural details of graft coverage, might play a more significant role in VSI occurrence. Significant TAD growth had occurred in all visceral segments. These results highlight the importance of lifelong surveillance following TEVAR and identified a subset of patients who might have an increased risk of reintervention., (Copyright © 2022 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.)

Purpose of the Program: This article provides guidance on optimizing the management of pediatric patients with end-stage kidney disease (ESKD) who will be or are being treated with any form of home or in-center dialysis during the COVID-19 pandemic. The goals are to provide the best possible care for pediatric patients with ESKD during the pandemic and ensure the health care team's safety., Sources of Information: The core of these rapid guidelines is derived from the Canadian Society of Nephrology (CSN) consensus recommendations for adult patients recently published in the Canadian Journal of Kidney Health and Disease ( CJKHD ). We also consulted specific documents from other national and international agencies focused on pediatric kidney health. Additional information was obtained by formal review of the published academic literature relevant to pediatric home or in-center hemodialysis., Methods: The Leadership of the Canadian Association of Paediatric Nephrologists (CAPN), which is affiliated with the CSN, solicited a team of clinicians and researchers with expertise in pediatric home and in-center dialysis. The goal was to adapt the guidelines recently adopted for Canadian adult dialysis patients for pediatric-specific settings. These included specific COVID-19-related themes that apply to dialysis in a Canadian environment, as determined by a group of senior renal leaders. Expert clinicians and nurses with deep expertise in pediatric home and in-center dialysis reviewed the revised pediatric guidelines., Key Findings: We identified 7 broad areas of home dialysis practice management that may be affected by the COVID-19 pandemic: (1) peritoneal dialysis catheter placement, (2) home dialysis training, (3) home dialysis management, (4) personal protective equipment, (5) product delivery, (6) minimizing direct health care providers and patient contact, and (7) caregivers support in the community. In addition, we identified 8 broad areas of in-center dialysis practice management that may be affected by the COVID-19 pandemic: (1) identification of patients with COVID-19, (2) hemodialysis of patients with confirmed COVID-19, (3) hemodialysis of patients not yet known to have COVID-19, (4) management of visitors to the dialysis unit, (5) handling COVID-19 testing of patients and staff, (6) safe practices during resuscitation procedures in a pandemic, (7) routine hemodialysis care, and (8) hemodialysis care under fixed dialysis resources. We make specific suggestions and recommendations for each of these areas., Limitations: At the time when we started this work, we knew that evidence on the topic of pediatric dialysis and COVID-19 would be severely limited, and our resources were also limited. We did not, therefore, do formal systematic review or meta-analysis. We did not evaluate our specific suggestions in the clinical environment. Thus, this article's advice and recommendations are primarily expert opinions and subject to the biases associated with this level of evidence. To expedite the publication of this work, we created a parallel review process that may not be as robust as standard arms' length peer-review processes., Implications: We intend these recommendations to help provide the best care possible for pediatric patients prescribed in-center or home dialysis during the COVID-19 pandemic, a time of altered priorities and reduced resources., Competing Interests: Declaration of Conflicting Interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2021.)

Purpose: To collate best practice recommendations on the management of patients receiving in-center hemodialysis during the COVID-19 pandemic, based on published reports and current public health advice, while considering ethical principles and the unique circumstances of Canadian hemodialysis units across the country., Sources of Information: The workgroup members used Internet search engines to retrieve documents from provincial and local hemodialysis programs; provincial public health agencies; the Centers for Disease Control and Prevention; webinars and slides from other kidney agencies; and nonreviewed preprints. PubMed was used to search for peer-reviewed published articles. Informal input was sought from knowledge users during a webinar., Methods: Challenges in the care of hemodialysis patients during the COVID-19 pandemic were highlighted within the Canadian Senior Renal Leaders Forum discussion group. The Canadian Society of Nephrology (CSN) developed the COVID-19 rapid response team (RRT) to address these challenges. They identified a pan-Canadian team of clinicians and administrators with expertise in hemodialysis to form the workgroup. One lead was chosen who drafted the initial document. Members of the workgroup reviewed and discussed all recommendations in detail during 2 virtual meetings on April 7 and April 9. Disagreements were resolved by consensus. The document was reviewed by the CSN COVID-19 RRT, an ethicist, an infection control expert, a community nephrologist, and a patient partner. Content was presented during an interactive webinar on April 11, 2020 attended by 269 kidney health professionals, and the webinar and first draft of the document were posted online. Final revisions were made based on feedback received until April 13, 2020. CJKHD editors reviewed the parallel process peer review and edited the manuscript for clarity., Key Findings: Recommendations were made under the following themes: (1) Identification of patients with COVID-19 in the dialysis unit, (2) hemodialysis of patients with confirmed COVID-19, (3) hemodialysis of patients not yet known to have COVID-19, (4) visitors; (5) testing for COVID-19 in the dialysis unit; (6) resuscitation, (6) routine hemodialysis care, (7) hemodialysis care under fixed dialysis resources., Limitations: Because of limitations of time and resources, and the large number of questions, formal systematic review was not undertaken. The recommendations are based on expert opinion and subject to bias. The parallel review process that was created may not be as robust as the standard peer review process., Implications: We hope that these recommendations provide guidance for dialysis unit directors, clinicians, and administrators on how to limit risk from infection and adverse outcomes, while providing necessary dialysis care in a setting of finite resources. We also identify a number of resource allocation priorities, which we hope will inform decisions at provincial funding agencies., Competing Interests: Declaration of Conflicting Interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2020.)

Background: Patients with congenital heart disease have high heart transplant waitlist mortality, and mechanical support is suboptimal. To evaluate feasibility of cardiac grafts from a genetically engineered triple-knockout pig as a bridge to allotransplantation, preformed anti-pig antibodies were measured in pediatric and adult patients., Methods: Flow cytometry measured serum immunoglobulin M (IgM) or IgG binding to wild-type and triple-knockout red blood cells (RBCs), with binding to human O-negative RBCs as a negative control. Group 1 comprise 84 pediatric patients and 64 healthy adults' sera with no previous cardiac surgery. Group 2 comprised 25 infant's sera postcardiac surgery, including 10 after palliation for hypoplastic left heart syndrome., Results: In group 1, IgM binding to wild-type RBCs occurred in 80% of sera and IgG binding occurred in in 91% of sera. Only 3% of sera showed IgM binding to triple-knockout RBCs, and 1 (<1%) was weakly positive for IgG binding. In group 2, all 25 infants demonstrated increased IgM and IgG binding to wild-type RBCs. One patient showed minimal IgM and another showed low IgG binding to triple-knockout RBCs. No infant after stage 1 Norwood demonstrated any IgG or IgM binding., Conclusions: Preformed anti-pig antibodies may not be a barrier to heart xenotransplantation in infants, even after cardiac surgery. With adequate immunosuppressive therapy, a triple-knockout pig heart transplant might function successfully as a bridge to allotransplantation., (Copyright © 2020 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.)

ELL family transcription factors activate the overall rate of RNA polymerase II (Pol II) transcription elongation by binding directly to Pol II and suppressing its tendency to pause. In metazoa, ELL regulates Pol II transcription elongation as part of a large multisubunit complex referred to as the Super Elongation Complex (SEC), which includes P-TEFb and EAF, AF9 or ENL, and an AFF family protein. Although orthologs of ELL and EAF have been identified in lower eukaryotes including Schizosaccharomyces pombe, it has been unclear whether SEC-like complexes function in lower eukaryotes. In this report, we describe isolation from S. pombe of an ELL-containing complex with features of a rudimentary SEC. This complex includes S. pombe Ell1, Eaf1, and a previously uncharacterized protein we designate Ell1 binding protein 1 (Ebp1), which is distantly related to metazoan AFF family members. Like the metazoan SEC, this S. pombe ELL complex appears to function broadly in Pol II transcription. Interestingly, it appears to have a particularly important role in regulating genes involved in cell separation.

The NF-κB family of transcription factors is pivotal in controlling cellular responses to environmental stresses; abnormal nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling features in many autoimmune diseases and cancers. Several components of the NF-κB signaling pathway have been reported to interact with the protein TNIP2 (also known as ABIN2), and TNIP2 can both positively and negatively regulate NF-κB- dependent transcription of target genes. However, the function of TNIP2 remains elusive and the cellular machinery associating with TNIP2 has not been systematically defined. Here we first used a broad MudPIT/Halo Affinity Purification Mass Spectrometry (AP-MS) approach to map the network of proteins associated with the NF-κB transcription factors, and establish TNIP2 as an NF-κB network hub protein. We then combined AP-MS with biochemical approaches in a more focused study of truncated and mutated forms of TNIP2 to map protein associations with distinct regions of TNIP2. NF-κB interacted with the N-terminal region of TNIP2. A central region of TNIP2 interacted with the endosomal sorting complex ESCRT-I via its TSG101 subunit, a protein essential for HIV-1 budding, and a single point mutant in TNIP2 disrupted this interaction. The major gene ontology category for TNIP2 associated proteins was mRNA metabolism, and several of these associations, like KHDRBS1, were lost upon depletion of RNA. Given the major association of TNIP2 with mRNA metabolism proteins, we analyzed the RNA content of affinity purified TNIP2 using RNA-Seq. Surprisingly, a specific limited number of mRNAs was associated with TNIP2. These RNAs were enriched for transcription factor binding, transcription factor cofactor activity, and transcription regulator activity. They included mRNAs of genes in the Sin3A complex, the Mediator complex, JUN, HOXC6, and GATA2. Taken together, our findings suggest an expanded role for TNIP2, establishing a link between TNIP2, cellular transport machinery, and RNA transcript processing., Competing Interests: The authors declare that they have no conflict of interest., (© 2016 by The American Society for Biochemistry and Molecular Biology, Inc.)

RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down of 12 nuclear and cytoplasmic RBPs followed by quantitative mass spectrometry (MS) demonstrates that proteins interacting with multiple RBPs in an RNA-dependent manner are enriched for RBPs. This motivated SONAR, a computational approach that predicts RNA binding activity by analyzing large-scale affinity precipitation-MS protein-protein interactomes. Without relying on sequence or structure information, SONAR identifies 1,923 human, 489 fly, and 745 yeast RBPs, including over 100 human candidate RBPs that contain zinc finger domains. Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Proteins that respond to DNA damage play critical roles in normal and diseased states in human biology. Studies have suggested that the S. cerevisiae protein CMR1/YDL156w is associated with histones and is possibly associated with DNA repair and replication processes. Through a quantitative proteomic analysis of affinity purifications here we show that the human homologue of this protein, WDR76, shares multiple protein associations with the histones H2A, H2B, and H4. Furthermore, our quantitative proteomic analysis of WDR76 associated proteins demonstrated links to proteins in the DNA damage response like PARP1 and XRCC5 and heterochromatin related proteins like CBX1, CBX3, and CBX5. Co-immunoprecipitation studies validated these interactions. Next, quantitative imaging studies demonstrated that WDR76 was recruited to laser induced DNA damage immediately after induction, and we compared the recruitment of WDR76 to laser induced DNA damage to known DNA damage proteins like PARP1, XRCC5, and RPA1. In addition, WDR76 co-localizes to puncta with the heterochromatin proteins CBX1 and CBX5, which are also recruited to DNA damage but much less intensely than WDR76. This work demonstrates the chromatin and DNA damage protein associations of WDR76 and demonstrates the rapid response of WDR76 to laser induced DNA damage.

The highly conserved yeast R2TP complex, consisting of Rvb1, Rvb2, Pih1, and Tah1, participates in diverse cellular processes ranging from assembly of protein complexes to apoptosis. Rvb1 and Rvb2 are closely related proteins belonging to the AAA+ superfamily and are essential for cell survival. Although Rvbs have been shown to be associated with various protein complexes including the Ino80 and Swr1chromatin remodeling complexes, we performed a systematic quantitative proteomic analysis of their associated proteins and identified two additional complexes that associate with Rvb1 and Rvb2: the chaperonin-containing T-complex and the 19S regulatory particle of the proteasome complex. We also analyzed Rvb1 and Rvb2 purified from yeast strains devoid of PIH1 and TAH1. These analyses revealed that both Rvb1 and Rvb2 still associated with Hsp90 and were highly enriched with RNA polymerase II complex components. Our analyses also revealed that both Rvb1 and Rvb2 were recruited to the Ino80 and Swr1 chromatin remodeling complexes even in the absence of Pih1 and Tah1 proteins. Using further biochemical analysis, we showed that Rvb1 and Rvb2 directly interacted with Hsp90 as well as with the RNA polymerase II complex. RNA-Seq analysis of the deletion strains compared with the wild-type strains revealed an up-regulation of ribosome biogenesis and ribonucleoprotein complex biogenesis genes, down-regulation of response to abiotic stimulus genes, and down-regulation of response to temperature stimulus genes. A Gene Ontology analysis of the 80 proteins whose protein associations were altered in the PIH1 or TAH1 deletion strains found ribonucleoprotein complex proteins to be the most enriched category. This suggests an important function of the R2TP complex in ribonucleoprotein complex biogenesis at both the proteomic and genomic levels. Finally, these results demonstrate that deletion network analyses can provide novel insights into cellular systems., (© 2016 by The American Society for Biochemistry and Molecular Biology, Inc.)

A common approach for exploring the interactome, the network of protein-protein interactions in cells, uses a commercially available ORF library to express affinity tagged bait proteins; these can be expressed in cells and endogenous cellular proteins that copurify with the bait can be identified as putative interacting proteins using mass spectrometry. Control experiments can be used to limit false-positive results, but in many cases, there are still a surprising number of prey proteins that appear to copurify specifically with the bait. Here, we have identified one source of false-positive interactions in such studies. We have found that a combination of: 1) the variable sequence of the C-terminus of the bait with 2) a C-terminal valine "cloning scar" present in a commercially available ORF library, can in some cases create a peptide motif that results in the aberrant co-purification of endogenous cellular proteins. Control experiments may not identify false positives resulting from such artificial motifs, as aberrant binding depends on sequences that vary from one bait to another. It is possible that such cryptic protein binding might occur in other systems using affinity tagged proteins; this study highlights the importance of conducting careful follow-up studies where novel protein-protein interactions are suspected.

The development of affinity purification technologies combined with mass spectrometric analysis of purified protein mixtures has been used both to identify new protein-protein interactions and to define the subunit composition of protein complexes. Transcription factor protein interactions, however, have not been systematically analyzed using these approaches. Here, we investigated whether ectopic expression of an affinity tagged transcription factor as bait in affinity purification mass spectrometry experiments perturbs gene expression in cells, resulting in the false positive identification of bait-associated proteins when typical experimental controls are used. Using quantitative proteomics and RNA sequencing, we determined that the increase in the abundance of a set of proteins caused by overexpression of the transcription factor RelA is not sufficient for these proteins to then co-purify non-specifically and be misidentified as bait-associated proteins. Therefore, typical controls should be sufficient, and a number of different baits can be compared with a common set of controls. This is of practical interest when identifying bait interactors from a large number of different baits. As expected, we found several known RelA interactors enriched in our RelA purifications (NFκB1, NFκB2, Rel, RelB, IκBα, IκBβ, and IκBε). We also found several proteins not previously described in association with RelA, including the small mitochondrial chaperone Tim13. Using a variety of biochemical approaches, we further investigated the nature of the association between Tim13 and NFκB family transcription factors. This work therefore provides a conceptual and experimental framework for analyzing transcription factor protein interactions., (© 2014 by The American Society for Biochemistry and Molecular Biology, Inc.)

Saliva is known to play a crucial role in insect feeding behavior and virus transmission. Currently, little is known about the salivary glands and saliva of thrips, despite the fact that Frankliniella occidentalis (Pergande) (the western flower thrips) is a serious pest due to its destructive feeding, wide host range, and transmission of tospoviruses. As a first step towards characterizing thrips salivary gland functions, we sequenced the transcriptome of the primary salivary glands of F. occidentalis using short read sequencing (Illumina) technology. A de novo-assembled transcriptome revealed 31,392 high quality contigs with an average size of 605 bp. A total of 12,166 contigs had significant BLASTx or tBLASTx hits (E≤1.0E-6) to known proteins, whereas a high percentage (61.24%) of contigs had no apparent protein or nucleotide hits. Comparison of the F. occidentalis salivary gland transcriptome (sialotranscriptome) against a published F. occidentalis full body transcriptome assembled from Roche-454 reads revealed several contigs with putative annotations associated with salivary gland functions. KEGG pathway analysis of the sialotranscriptome revealed that the majority (18 out of the top 20 predicted KEGG pathways) of the salivary gland contig sequences match proteins involved in metabolism. We identified several genes likely to be involved in detoxification and inhibition of plant defense responses including aldehyde dehydrogenase, metalloprotease, glucose oxidase, glucose dehydrogenase, and regucalcin. We also identified several genes that may play a role in the extra-oral digestion of plant structural tissues including β-glucosidase and pectin lyase; and the extra-oral digestion of sugars, including α-amylase, maltase, sucrase, and α-glucosidase. This is the first analysis of a sialotranscriptome for any Thysanopteran species and it provides a foundational tool to further our understanding of how thrips interact with their plant hosts and the viruses they transmit.

Promoter-proximal pausing by initiated RNA polymerase II (Pol II) and regulated release of paused polymerase into productive elongation has emerged as a major mechanism of transcription activation. Reactivation of paused Pol II correlates with recruitment of super-elongation complexes (SECs) containing ELL/EAF family members, P-TEFb, and other proteins, but the mechanism of their recruitment is an unanswered question. Here, we present evidence for a role of human Mediator subunit MED26 in this process. We identify in the conserved N-terminal domain of MED26 overlapping docking sites for SEC and a second ELL/EAF-containing complex, as well as general initiation factor TFIID. In addition, we present evidence consistent with the model that MED26 can function as a molecular switch that interacts first with TFIID in the Pol II initiation complex and then exchanges TFIID for complexes containing ELL/EAF and P-TEFb to facilitate transition of Pol II into the elongation stage of transcription., (Copyright © 2011 Elsevier Inc. All rights reserved.)

The proteasome degrades proteins modified by polyubiquitylation, so correctly controlled ubiquitylation is crucial to avoid unscheduled proteolysis of essential proteins. The mechanism regulating proteolysis of RNAPII has been controversial since two distinct ubiquitin ligases (E3s), Rsp5 (and its human homologue NEDD4) and Elongin-Cullin complex, have both been shown to be required for its DNA-damage-induced polyubiquitylation. Here we show that these E3s work sequentially in a two-step mechanism. First, Rsp5 adds mono-ubiquitin, or sometimes a ubiquitin chain linked via ubiquitin lysine 63 that does not trigger proteolysis. When produced, the K63 chain can be trimmed to mono-ubiquitylation by an Rsp5-associated ubiquitin protease, Ubp2. Based on this mono-ubiquitin moiety on RNAPII, an Elc1/Cul3 complex then produces a ubiquitin chain linked via lysine 48, which can trigger proteolysis. Likewise, for correct polyubiquitylation of human RNAPII, NEDD4 cooperates with the ElonginA/B/C-Cullin 5 complex. These data indicate that RNAPII polyubiquitylation requires cooperation between distinct, sequentially acting ubiquitin ligases, and raise the intriguing possibility that other members of the large and functionally diverse family of NEDD4-like ubiquitin ligases also require the assistance of a second E3 when targeting proteins for degradation.

ELL family transcription factors activate the rate of transcript elongation by suppressing transient pausing by RNA polymerase II at many sites along the DNA. ELL-associated factors 1 and 2 (EAF1 and EAF2) bind stably to ELL family members and act as strong positive regulators of their transcription activities. Orthologs of ELL and EAF have been identified in metazoa, but it has been unclear whether such RNA polymerase II elongation factors are utilized in lower eukaryotes. Using bioinformatic and biochemical approaches, we have identified a new Schizosaccharomyces pombe RNA polymerase II elongation factor that is composed of two subunits designated SpELL and SpEAF, which share weak sequence similarity with members of the metazoan ELL and EAF families. Like mammalian ELL-EAF, SpELL-SpEAF stimulates RNA polymerase II transcription elongation and pyrophosphorolysis. In addition, like many yeast RNA polymerase II elongation factors, deletion of the SpELL gene renders S. pombe sensitive to the drug 6-azauracil. Finally, phylogenetic analyses suggest that the SpELL and SpEAF proteins are evolutionarily conserved in many fungi but not in Saccharomyces cerevisiae.

In human cells, the ELL family of transcription factors includes at least three members, which are all capable of stimulating the overall rate of elongation by RNA polymerase II by suppressing transient pausing by the enzyme at many sites along DNA. In this report, we identify the ELL-associated factors (EAF)1 and EAF2 as strong positive regulators of ELL elongation activity. Our findings provide insights into the structure and function of ELL family transcription factors, and they bring to light direct roles for the EAF proteins in regulation of RNA polymerase II transcription.

The ankyrin repeat-containing protein with a suppressor of cytokine signaling box-2 (ASB2) gene was identified as a retinoic acid-response gene and a target of the promyelocytic leukemia-retinoic acid receptor-alpha oncogenic protein characteristic of acute promyelocytic leukemia. Expression of ASB2 in myeloid leukemia cells inhibits growth and promotes commitment, recapitulating an early step known to be critical for differentiation. Here we show that ASB2, by interacting with the Elongin BC complex, can assemble with Cullin5.Rbx1 to form an E3 ubiquitin ligase complex that stimulates polyubiquitination by the E2 ubiquitin-conjugating enzyme Ubc5. This is a first indication that a member of the ASB protein family, ASB2, is a subunit of an ECS (Elongin C-Cullin-SOCS box)-type E3 ubiquitin ligase complex. Altogether, our results strongly suggest that ASB2 targets specific proteins to destruction by the proteasome in leukemia cells that have been induced to differentiate.

The multiprotein Mediator (Med) complex is an evolutionarily conserved transcriptional regulator that plays important roles in activation and repression of RNA polymerase II transcription. Prior studies identified a set of more than twenty distinct polypeptides that compose the Saccharomyces cerevisiae Mediator. Here we discuss efforts to characterize the subunit composition and associated activities of the mammalian Med complex.

The Mediator is a multiprotein transcriptional coactivator that is expressed ubiquitously in eukaryotes from yeast to mammals and is required for induction of RNA polymerase II (pol II) transcription by DNA binding transcription factors. In the work described here, we exploit multidimensional protein identification technology (MudPIT) to carry out a proteomic analysis of the subunit composition of the mammalian Mediator complex. By comparing MudPIT data sets obtained from six independent Mediator preparations immunoaffinity purified through their Nut2 (MED10), Med25 (MED9), Intersex (MED29), LCMR1 (MED19), AK007855 (MED28), or CRSP70 (MED26) subunits, we identify a set of consensus mammalian Mediator subunits. In addition, we identify as Mediator-associated proteins the CDK8-like cyclin-dependent kinase CDK11 and the TRAP240-like KIAA1025 protein (MED13L), which is mutated in patients with the congenital heart defect transposition of the great arteries (TGA).

The multiprotein Mediator complex is a coactivator required for activation of RNA polymerase II transcription by DNA bound transcription factors. We previously identified and partially purified a mammalian Mediator complex from rat liver nuclei (Brower, C.S., Sato, S., Tomomori-Sato, C., Kamura, T., Pause, A., Stearman, R., Klausner, R.D., Malik, S., Lane, W.S., Sorokina, I., Roeder, R.G., Conaway, J.W., and Conaway, R.C. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 10353-10358). Analysis by tandem mass spectrometry of proteins present in the most highly purified rat Mediator fractions led to the identification of a collection of new mammalian Mediator subunits, as well as several potential Mediator subunits including a previously uncharacterized protein encoded by the FLJ10193 open reading frame. In this study, we present direct biochemical evidence that the FLJ10193 protein, which we designate Med25, is a bona fide subunit of the mammalian Mediator complex. In addition, we present evidence that Med25 shares structural and functional properties with Saccharomyces cerevisiae Mediator subunit Cse2 and may be a mammalian Cse2 ortholog. Taken together, our findings identify a novel mammalian Mediator subunit and shed new light on the architecture of the mammalian Mediator complex.

The multiprotein Mediator complex is a coactivator required for transcriptional activation of RNA polymerase II transcribed genes by DNA binding transcription factors. We previously partially purified a Med8-containing Mediator complex from rat liver nuclei (Brower, C. S., Sato, S., Tomomori-Sato, C., Kamura, T., Pause, A., Stearman, R., Klausner, R. D., Malik, S., Lane, W. S., Sorokina, I., Roeder, R. G., Conaway, J. W., and Conaway, R. C. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 10353-10358). Analysis of proteins present in the most highly enriched Mediator fractions by tandem mass spectrometry led to the identification of several new mammalian Mediator subunits, as well as several potential Mediator subunits. Here we identify one of these proteins, encoded by the previously uncharacterized AK000411 open reading frame, as a new subunit of the mammalian Mediator complex. The AK000411 protein, which we designate hIntersex (human Intersex), shares significant sequence similarity with the Drosophila melanogaster intersex protein, which has functional properties expected of a transcriptional coactivator specific for the Drosophila doublesex transactivator. In addition, we show that hIntersex assembles into a subcomplex with Mediator subunits p28b and TRFP. Taken together, our findings identify a new subunit of the mammalian Mediator and shed new light on the architecture of the mammalian Mediator complex.

The Mediator is a multiprotein coactivator required for activation of RNA polymerase II transcription by DNA binding transactivators. We recently identified a mammalian homologue of yeast Mediator subunit Med8 and partially purified a Med8-containing Mediator complex from rat liver nuclei (Brower, C. S., Sato, S., Tomomori-Sato, C., Kamura, T., Pause, A., Stearman, R., Klausner, R. D., Malik, S., Lane, W. S., Sorokina, I., Roeder, R. G., Conaway, J. W., and Conaway, R. C. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 10353-10358). Analysis of proteins present in the most highly purified Med8-containing fractions by tandem mass spectrometry led to the identification of many known mammalian Mediator subunits, as well as four potential Mediator subunits exhibiting sequence similarity to yeast Mediator subunits Srb5, Srb6, Med11, and Rox3. Here we present direct biochemical evidence that these four proteins are bona fide mammalian Mediator subunits. In addition, we identify direct pairwise binding partners of these proteins among the known mammalian Mediator subunits. Taken together, our findings identify a collection of novel mammalian Mediator subunits and shed new light on the underlying architecture of the mammalian Mediator complex.