Network trade-offs and homeostasis in Arabidopsis shoot architectures.

Understanding the optimization objectives that shape shoot architectures remains a critical problem in plant biology. Here, we performed 3D scanning of 152 Arabidopsis shoot architectures, including wildtype and 10 mutant strains, and we uncovered a design principle that describes how architectures make trade-offs between competing objectives. First, we used graph-theoretic analysis to show that Arabidopsis shoot architectures strike a Pareto optimal that can be captured as maximizing performance in transporting nutrients and minimizing costs in building the architecture. Second, we identify small sets of genes that can be mutated to shift the weight prioritizing one objective over the other. Third, we show that this prioritization weight feature is significantly less variable across replicates of the same genotype compared to other common plant traits (e.g., number of rosette leaves, total volume occupied). This suggests that this feature is a robust descriptor of a genotype, and that local variability in structure may be compensated for globally in a homeostatic manner. Overall, our work provides a framework to understand optimization trade-offs made by shoot architectures and provides evidence that these trade-offs can be modified genetically, which may aid plant breeding and selection efforts.

Transcription-translation coupling: direct interactions of RNA polymerase with ribosomes and ribosomal subunits.

In prokaryotes, RNA polymerase and ribosomes can bind concurrently to the same RNA transcript, leading to the functional coupling of transcription and translation. The interactions between RNA polymerase and ribosomes are crucial for the coordination of transcription with translation. Here, we report that RNA polymerase directly binds ribosomes and isolated large and small ribosomal subunits. RNA polymerase and ribosomes form a one-to-one complex with a micromolar dissociation constant. The formation of the complex is modulated by the conformational and functional states of RNA polymerase and the ribosome. The binding interface on the large ribosomal subunit is buried by the small subunit during protein synthesis, whereas that on the small subunit remains solvent-accessible. The RNA polymerase binding site on the ribosome includes that of the isolated small ribosomal subunit. This direct interaction between RNA polymerase and ribosomes may contribute to the coupling of transcription to translation.

Two Old Dogs, One New Trick: A Review of RNA Polymerase and Ribosome Interactions during Transcription-Translation Coupling.

The coupling of transcription and translation is more than mere translation of an mRNA that is still being transcribed. The discovery of physical interactions between RNA polymerase and ribosomes has spurred renewed interest into this long-standing paradigm of bacterial molecular biology. Here, we provide a concise presentation of recent insights gained from super-resolution microscopy, biochemical, and structural work, including cryo-EM studies. Based on the presented data, we put forward a dynamic model for the interaction between RNA polymerase and ribosomes, in which the interactions are repeatedly formed and broken. Furthermore, we propose that long intervening nascent RNA will loop out and away during the forming the interactions between the RNA polymerase and ribosomes. By comparing the effect of the direct interactions between RNA polymerase and ribosomes with those that transcription factors NusG and RfaH mediate, we submit that two distinct modes of coupling exist: Factor-free and factor-mediated coupling. Finally, we provide a possible framework for transcription-translation coupling and elude to some open questions in the field.

A Metal-Organic Framework with Cooperative Phosphines That Permit Post-Synthetic Installation of Open Metal Sites.

PCM-101 is a phosphine coordination material comprised of tris(p-carboxylato)triphenylphosphine and secondary pillaring groups coordinated to [M3 (OH)]5+ nodes (M=Co, Ni). PCM-101 has a unique topology in which R3 P: sites are arranged directly trans to one another, with a P⋅⋅⋅P separation distance dictated by the pillars. Post-synthetic coordination of soft metals to the P: sites proceeds at room temperature to provide X-ray quality crystals that permit full structural resolution. Addition of AuCl groups forces a large distortion of the parent framework. In contrast, CuBr undergoes insertion directly between the trans-P sites to form dimers that mimic solution-phase complexes, but that are geometrically strained due to steric pressure exerted by the MOF scaffold. The metalated materials are active in heterogeneous hydroaddition catalysis under mild conditions, yielding different major products compared to their molecular counterparts.

Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion to enable the retrotranslocation of ERAD membrane substrates.

Nearly one-third of proteins are initially targeted to the endoplasmic reticulum (ER) membrane, where they are correctly folded and then delivered to their final cellular destinations. To prevent the accumulation of misfolded membrane proteins, ER-associated degradation (ERAD) moves these clients from the ER membrane to the cytosol, a process known as retrotranslocation. Our recent work in Saccharomyces cerevisiae reveals a derlin rhomboid pseudoprotease, Dfm1, is involved in the retrotranslocation of ubiquitinated ERAD membrane substrates. In this study, we identify conserved residues of Dfm1 that are critical for retrotranslocation. We find several retrotranslocation-deficient Loop 1 mutants that display impaired binding to membrane substrates. Furthermore, Dfm1 possesses lipid thinning function to facilitate in the removal of ER membrane substrates, and this feature is conserved in its human homolog, Derlin-1, further implicating that derlin-mediated retrotranslocation is a well-conserved process.

Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA.

While genome recoding using quadruplet codons to incorporate non-proteinogenic amino acids is attractive for biotechnology and bioengineering purposes, the mechanism through which such codons are translated is poorly understood. Here we investigate translation of quadruplet codons by a +1-frameshifting tRNA, SufB2, that contains an extra nucleotide in its anticodon loop. Natural post-transcriptional modification of SufB2 in cells prevents it from frameshifting using a quadruplet-pairing mechanism such that it preferentially employs a triplet-slippage mechanism. We show that SufB2 uses triplet anticodon-codon pairing in the 0-frame to initially decode the quadruplet codon, but subsequently shifts to the +1-frame during tRNA-mRNA translocation. SufB2 frameshifting involves perturbation of an essential ribosome conformational change that facilitates tRNA-mRNA movements at a late stage of the translocation reaction. Our results provide a molecular mechanism for SufB2-induced +1 frameshifting and suggest that engineering of a specific ribosome conformational change can improve the efficiency of genome recoding.

A Statistical Growth Property of Plant Root Architectures.

Numerous types of biological branching networks, with varying shapes and sizes, are used to acquire and distribute resources. Here, we show that plant root and shoot architectures share a fundamental design property. We studied the spatial density function of plant architectures, which specifies the probability of finding a branch at each location in the 3-dimensional volume occupied by the plant. We analyzed 1645 root architectures from four species and discovered that the spatial density functions of all architectures are population-similar. This means that despite their apparent visual diversity, all of the roots studied share the same basic shape, aside from stretching and compression along orthogonal directions. Moreover, the spatial density of all architectures can be described as variations on a single underlying function: a Gaussian density truncated at a boundary of roughly three standard deviations. Thus, the root density of any architecture requires only four parameters to specify: the total mass of the architecture and the standard deviations of the Gaussian in the three (x, y, z) growth directions. Plant shoot architectures also follow this design form, suggesting that two basic plant transport systems may use similar growth strategies.

Expansion of the Major Facilitator Superfamily (MFS) to include novel transporters as well as transmembrane-acting enzymes.

The Major Facilitator Superfamily (MFS) is currently the largest characterized superfamily of transmembrane secondary transport proteins. Its diverse members are found in essentially all organisms in the biosphere and function by uniport, symport, and/or antiport mechanisms. In 1993 we first named and described the MFS which then consisted of 5 previously known families that had not been known to be related, and by 2012 we had identified a total of 74 families, classified phylogenetically within the MFS, all of which included only transport proteins. This superfamily has since expanded to 89 families, all included under TC# 2.A.1, and a few transporter families outside of TC# 2.A.1 were identified as members of the MFS. In this study, we assign nine previously unclassified protein families in the Transporter Classification Database (TCDB; http://www.tcdb.org) to the MFS based on multiple criteria and bioinformatic methodologies. In addition, we find integral membrane domains distantly related to partial or full-length MFS permeases in Lysyl tRNA Synthases (TC# 9.B.111), Lysylphosphatidyl Glycerol Synthases (TC# 4.H.1), and cytochrome b561 transmembrane electron carriers (TC# 5.B.2). Sequence alignments, overlap of hydropathy plots, compatibility of repeat units, similarity of complexity profiles of transmembrane segments, shared protein domains and 3D structural similarities between transport proteins were analyzed to assist in inferring homology. The MFS now includes 105 families.

High-Resolution Laser Scanning Reveals Plant Architectures that Reflect Universal Network Design Principles.

Transport networks serve critical functions in biological and engineered systems, and yet their design requires trade-offs between competing objectives. Due to their sessile lifestyle, plants need to optimize their architecture to efficiently acquire and distribute resources while also minimizing costs in building infrastructure. To understand how plants resolve this design trade-off, we used high-precision three-dimensional laser scanning to map the architectures of tomato, tobacco, or sorghum plants grown in several environmental conditions and through multiple developmental time points, scanning in total 505 architectures from 37 plants. Using a graph-theoretic algorithm that we developed to evaluate design strategies, we find that plant architectures lie along the Pareto front between two simple length-based objectives-minimizing total branch length and minimizing nutrient transport distance-thereby conferring a selective fitness advantage for plant transport processes. The location along the Pareto front can distinguish among species and conditions, suggesting that during evolution, natural selection may employ common network design principles despite different optimization trade-offs.

A Statistical Description of Plant Shoot Architecture.

Plant architectures can be characterized statistically by their spatial density function, which specifies the probability of finding a branch at each location in the territory occupied by a plant. Using high-precision 3D scanning, we analyzed 557 plant shoot architectures, representing three species, grown across three to five environmental conditions, and through 20-30 developmental time points. We found two elegant properties in the spatial density functions of these architectures: all functions could be nearly modified in one direction without affecting the density in orthogonal directions (called "separability"), and all functions shared the same underlying shape, aside from stretching and compression (called "self-similarity"). Surprisingly, despite their striking visual diversity, we discovered that all architectures could be described as variations on a single underlying function: a Gaussian density function truncated at roughly two SDs. We also observed systematic variation in the spatial density functions across species, growth conditions, and time, which suggests functional specialization despite following the same general design form.

Direct peritoneal resuscitation as adjunct to conventional resuscitation from hemorrhagic shock: a better outcome.

BACKGROUND: Conventional resuscitation (CR) from hemorrhagic shock often culminates in multisystem organ failure and death, commonly attributed to a progressive splanchnic vasoconstriction and hypoperfusion, a gut-derived systemic inflammatory response (SIR), and fluid sequestration. Direct peritoneal resuscitation (DPR) produces a sustained state of tissue hyperperfusion in splanchnic and distant organs. In this study we evaluated the therapeutic potential of DPR on the SIR and fluid sequestration as parameters of treatment outcome. METHODS: Anesthetized nonheparinized rats continuously monitored for hemodynamics were bled to 40% of mean arterial pressure for 60 minutes. Animals were randomized for CR or CR plus DPR under aseptic conditions. Sham nonhemorrhaged rats served as control. Qualitatively, animals were blindly observed for body weight, illness score, or death for 72 hours. Tissues were harvested from survivors, and SIR was measured by interleukin (IL)-6, IL-10, tumor necrosis factor-alpha, and enzyme-linked immunosorbent assay, and fluid sequestration was measured by dry weight/wet weight ratio (DW/WW). RESULTS: Adjunct DPR caused a marked increase (P >.01 by analysis of variance) in the immunoregulator IL-10 in the liver (10,990 +/- 1,470 pg/g) and gut (1815 +/- 640 pg/g), compared to CR rats (6450 +/- 1000 pg/g and 1555 +/- 590, respectively), which is associated with down-regulation of IL-6 and tumor necrosis factor-alpha in liver and gut, from 57 +/- 4 and 20 +/- 3 pg/g, respectively, to 42 +/- 4 and 9 +/- 2 pg/g in DPR-treated animals. CR animals had a lower DW/WW ratio in liver (-36%), spleen (-22%), and lung (-24%) compared to DPR (P <.05), where the DW/WW ratio did not differ from control animals. This fluid sequestration is consistent with a 12% and 5% gain in prehemorrhage body weight at 24 and 72 hours after treatment in the CR animals. Thirty percent of CR animals died within 24 hours, and survivors were squeaking, cold, and pale in eyes and ears and oliguric despite features of fluid overload. In comparison, DPR animals exhibited normal appearance by 24 hours and demonstrated a 100% survival at 72 hours. CONCLUSIONS: This study demonstrates that DPR as adjunct to CR has beneficial effects on the pathophysiology of resuscitated hemorrhagic shock. In addition to restoration of tissue perfusion, DPR has immunomodulation and anti-fluid sequestration effects. These modulations result in improved outcome.