O registro contínuo de 1.3 milhões de anos de hidroclima na África Oriental, e as implicações para padrões de evolução e biodiversidade

terça-feira, dezembro 08, 2015

Continuous 1.3-million-year record of East African hydroclimate, and implications for patterns of evolution and biodiversity

Robert P. Lyons a,1, Christopher A. Scholz 2,3, Andrew S. Cohen b, John W. King c, Erik T. Brown d, Sarah J. Ivory e, Thomas C. Johnson d, Alan L. Deino f, Peter N. Reinthal g, Michael M. McGlue h, and Margaret W. Blome b,3

aDepartment of Earth Sciences, Syracuse University, Syracuse, NY 13244;

bDepartment of Geosciences, University of Arizona, Tucson, AZ 85721;

cGraduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882;

dLarge Lakes Observatory and Department of Earth and Environmental Sciences, University of Minnesota, Duluth, MN 55812;

eInstitute at Brown for the Study of the Environment and Society, Brown University, Providence, RI 02912;

fBerkeley Geochronology Center, Berkeley, CA 94709;

gDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721;

hDepartment of Earth and Environmental Sciences, University of Kentucky, Lexington, KY 40506

Edited by Mark H. Thiemens, University of California, San Diego, La Jolla, CA, and approved October 29, 2015 (received for review June 30, 2015)


Significance

Lake Malawi is one of the world’s oldest and deepest lakes, with >1,000 species of endemic cichlid fish; its water bottom anoxia prevents bioturbation of deep-water sediments, which preserve exceptional paleoclimate signals. The Lake Malawi Drilling Project recovered the first continuous 1.3-My record of past climates of the African interior. These sediments show that the catchment experienced 24 dry periods over that time, when lake levels dropped more than 200 m. After ∼800,000 years ago, the lake was commonly deeper and overflowing, indicating wetter conditions, but lowstand intervals became more prolonged and extreme. These changes promoted the evolution of the endemic cichlid fishes, through shifting of habitats, and through isolation and restriction of populations.

Abstract

The transport of moisture in the tropics is a critical process for the global energy budget and on geologic timescales, has markedly influenced continental landscapes, migratory pathways, and biological evolution. Here we present a continuous, first-of-its-kind 1.3-My record of continental hydroclimate and lake-level variability derived from drill core data from Lake Malawi, East Africa (9–15° S). Over the Quaternary, we observe dramatic shifts in effective moisture, resulting in large-scale changes in one of the world’s largest lakes and most diverse freshwater ecosystems. Results show evidence for 24 lake level drops of more than 200 m during the Late Quaternary, including 15 lowstands when water levels were more than 400 m lower than modern. A dramatic shift is observed at the Mid-Pleistocene Transition (MPT), consistent with far-field climate forcing, which separates vastly different hydroclimate regimes before and after ∼800,000 years ago. Before 800 ka, lake levels were lower, indicating a climate drier than today, and water levels changed frequently. Following the MPT high-amplitude lake level variations dominate the record. From 800 to 100 ka, a deep, often overfilled lake occupied the basin, indicating a wetter climate, but these highstands were interrupted by prolonged intervals of extreme drought. Periods of high lake level are observed during times of high eccentricity. The extreme hydroclimate variability exerted a profound influence on the Lake Malawi endemic cichlid fish species flock; the geographically extensive habitat reconfiguration provided novel ecological opportunities, enabling new populations to differentiate rapidly to distinct species.

Lake Malawi tropical paleoclimatology East African rift cichlid fish quaternary

Footnotes

1Present address: Chevron Corporation, Houston, TX 77002.

2To whom correspondence should be addressed. Email: cascholz{at}syr.edu.

3Present address: BP L48 Onshore, Houston, TX 77079.

Author contributions: C.A.S., A.S.C., J.W.K., and T.C.J. designed research; R.P.L., C.A.S., A.S.C., J.W.K., E.T.B., S.J.I., T.C.J., P.N.R., M.M.M., and M.W.B. performed research; J.W.K., E.T.B., and A.L.D. contributed new reagents/analytic tools; R.P.L., C.A.S., A.S.C., J.W.K., E.T.B., S.J.I., T.C.J., A.L.D., M.M.M., and M.W.B. analyzed data; and R.P.L., C.A.S., A.S.C., T.C.J., and P.N.R. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: The paleoclimate proxy data and geochronology data have been deposited with the NOAA paleoclimatology database of the National Centers for Environmental Information:

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1512864112/-/DCSupplemental.

Freely available online through the PNAS open access option.

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Close up de citoesqueleto bacteriano em nível atômico-molecular

Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR

Chaowei Shi1,†, Pascal Fricke1,†, Lin Lin2,3,‡, Veniamin Chevelkov1, Melanie Wegstroth4, Karin Giller4, Stefan Becker4, Martin Thanbichler2,3,5 and Adam Lange1,6,§

- Author Affiliations

1Department of Molecular Biophysics, Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany.
2Prokaryotic Cell Biology Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.
3Faculty of Biology, Philipps-Universität, 35043 Marburg, Germany.
4Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
5LOEWE Center for Synthetic Microbiology, Philipps-Universität, 35043 Marburg, Germany.
6Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.

↵§Corresponding author. E-mail: alange@fmp-berlin.de

↵* Presented in part at the Gordon Research Conference “Computational Aspects—Biomolecular NMR” (Il Ciocco, 7 to 12 June 2015).

↵† These authors contributed equally to this work.

↵‡ Present address: Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland.

Science Advances  04 Dec 2015:
Vol. 1, no. 11, e1501087
DOI: 10.1126/sciadv.1501087


Abstract

Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the species Caulobacter crescentus is not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR–derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.
KeywordsCytoskeletal proteinsBactofilinsProtein StructureSolid-state NMR

Copyright © 2015, The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

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Ontogenia do maxilar nos Neandertais e seus ancestrais

segunda-feira, dezembro 07, 2015

Ontogeny of the maxilla in Neanderthals and their ancestors

Rodrigo S. Lacruz, Timothy G. Bromage, Paul O’Higgins, Juan-Luis Arsuaga, Chris Stringer, Ricardo Miguel Godinho, Johanna Warshaw, Ignacio Martínez, Ana Gracia-Tellez, José María Bermúdez de Castro & Eudald Carbonell

Affiliations Contributions Corresponding author

Nature Communications 6, Article number: 8996 doi:10.1038/ncomms9996

Received 13 August 2015 Accepted 23 October 2015 Published 07 December 2015


Schematic illustrates the principal growth direction of the maxilla in the Sima de los Huesos (SH) fossils, Neanderthals and modern humans. 

Abstract

Neanderthals had large and projecting (prognathic) faces similar to those of their putative ancestors from Sima de los Huesos (SH) and different from the retracted modern human face. When such differences arose during development and the morphogenetic modifications involved are unknown. We show that maxillary growth remodelling (bone formation and resorption) of the Devil’s Tower (Gibraltar 2) and La Quina 18 Neanderthals and four SH hominins, all sub-adults, show extensive bone deposition, whereas in modern humans extensive osteoclastic bone resorption is found in the same regions. This morphogenetic difference is evident by ~5 years of age. Modern human faces are distinct from those of the Neanderthal and SH fossils in part because their postnatal growth processes differ markedly. The growth remodelling identified in these fossil hominins is shared with Australopithecus and early Homo but not with modern humans suggesting that the modern human face is developmentally derived.

Subject terms: Biological sciences Evolution Palaeontology

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A fauna de Ediacara: a origem dos animais e uma hipótese 'Savana' para a evolução dos bilatérios

The origin of the animals and a ‘Savannah’ hypothesis for early bilaterian evolution

Graham E. Budd1,* and Sören Jensen2

Article first published online: 20 NOV 2015

DOI: 10.1111/brv.12239

© 2015 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Keywords: 

Cambrian explosion; ediacarans; ecology; heterogeneity; stem groups; Kimberella; evolution; trace fossils; animal origins; Apoikozoa


ABSTRACT

The earliest evolution of the animals remains a taxing biological problem, as all extant clades are highly derived and the fossil record is not usually considered to be helpful. The rise of the bilaterian animals recorded in the fossil record, commonly known as the ‘Cambrian explosion’, is one of the most significant moments in evolutionary history, and was an event that transformed first marine and then terrestrial environments. We review the phylogeny of early animals and other opisthokonts, and the affinities of the earliest large complex fossils, the so-called ‘Ediacaran’ taxa. We conclude, based on a variety of lines of evidence, that their affinities most likely lie in various stem groups to large metazoan groupings; a new grouping, the Apoikozoa, is erected to encompass Metazoa and Choanoflagellata. The earliest reasonable fossil evidence for total-group bilaterians comes from undisputed complex trace fossils that are younger than about 560 Ma, and these diversify greatly as the Ediacaran–Cambrian boundary is crossed a few million years later. It is generally considered that as the bilaterians diversified after this time, their burrowing behaviour destroyed the cyanobacterial mat-dominated substrates that the enigmatic Ediacaran taxa were associated with, the so-called ‘Cambrian substrate revolution’, leading to the loss of almost all Ediacara-aspect diversity in the Cambrian. Why, though, did the energetically expensive and functionally complex burrowing mode of life so typical of later bilaterians arise? Here we propose a much more positive relationship between late-Ediacaran ecologies and the rise of the bilaterians, with the largely static Ediacaran taxa acting as points of concentration of organic matter both above and below the sediment surface. The breaking of the uniformity of organic carbon availability would have signalled a decisive shift away from the essentially static and monotonous earlier Ediacaran world into the dynamic and burrowing world of the Cambrian. The Ediacaran biota thus played an enabling role in bilaterian evolution similar to that proposed for the Savannah environment for human evolution and bipedality. Rather than being obliterated by the rise of the bilaterians, the subtle remnants of Ediacara-style taxa within the Cambrian suggest that they remained significant components of Phanerozoic communities, even though at some point their enabling role for bilaterian evolution was presumably taken over by bilaterians or other metazoans. Bilaterian evolution was thus an essentially benthic event that only later impacted the planktonic environment and the style of organic export to the sea floor.

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Múltiplos processos de transporte proteico para os peroxissomas: mero acaso, fortuita necessidade ou design inteligente?

Journal of Molecular Biology
Volume 427, Issue 6, Part A, 27 March 2015, Pages 1176–1190
Elucidation of Protein Translocation Pathways (Part II)

Multiple Pathways for Protein Transport to Peroxisomes

P.K. Kim1, 2, E.H. Hettema3, , 

1 Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8

2 Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8

3 Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire S10 2TN, United Kingdom

Received 1 August 2014, Revised 5 February 2015, Accepted 6 February 2015, Available online 11 February 2015

Edited by S. High

Under a Creative Commons license

Highlights

• Peroxisomal membrane and matrix proteins require distinct factors for their transport.

• Matrix proteins fold in the cytosol prior to their import.

• Loaded targeting receptors form part of the matrix protein translocation pore.

• Many membrane proteins are directly inserted into the peroxisomal membrane.

• Some peroxisomal membrane proteins are transported via the ER to peroxisomes.


Abstract

Peroxisomes are unique among the organelles of the endomembrane system. Unlike other organelles that derive most if not all of their proteins from the ER (endoplasmic reticulum), peroxisomes contain dedicated machineries for import of matrix proteins and insertion of membrane proteins. However, peroxisomes are also able to import a subset of their membrane proteins from the ER. One aspect of peroxisome biology that has remained ill defined is the role the various import pathways play in peroxisome maintenance. In this review, we discuss the available data on matrix and membrane protein import into peroxisomes.




Abbreviations

PMP, peroxisomal membrane protein; PTS, peroxisomal targeting signal; TA, tail-anchored

Keywords

peroxisome; peroxin; protein import

Montagem do peroxissoma: matriz e biogênese da membrana proteica: mero acaso, fortuita necessidade ou design inteligente?

Published April 4, 2011 // JCB vol. 193 no. 1 7-16 

The Rockefeller University Press, doi: 10.1083/jcb.201010022

© 2011 Ma et al.

Review

Peroxisome assembly: matrix and membrane protein biogenesis

Changle Ma, Gaurav Agrawal, and Suresh Subramani

Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, CA 92093

Correspondence to Suresh Subramani: ssubramani{at}ucsd.edu

C. Ma and G. Agrawal contributed equally to this paper.


Abstract

The biogenesis of peroxisomal matrix and membrane proteins is substantially different from the biogenesis of proteins of other subcellular compartments, such as mitochondria and chloroplasts, that are of endosymbiotic origin. Proteins are targeted to the peroxisome matrix through interactions between specific targeting sequences and receptor proteins, followed by protein translocation across the peroxisomal membrane. Recent advances have shed light on the nature of the peroxisomal translocon in matrix protein import and the molecular mechanisms of receptor recycling. Furthermore, the endoplasmic reticulum has been shown to play an important role in peroxisomal membrane protein biogenesis. Defining the molecular events in peroxisome assembly may enhance our understanding of the etiology of human peroxisome biogenesis disorders.

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Poros distintos para importação peroxissomal de proteínas PTS1 e PTS2: mero acaso, fortuita necessidade ou design inteligente?

Cell Reports

Distinct Pores for Peroxisomal Import of PTS1 and PTS2 Proteins

Authors

Malayko Montilla-Martinez, Sabrina Beck, Jessica Klumper, Michael Meinecke, Wolfgang Schliebs, Richard Wagner, Ralf Erdmann

Correspondence

ri.wagner@jacobs-university.de (R.W.), ralf.erdmann@rub.de (R.E.)


In Brief

Two peroxisomal targeting signals, PTS1 and PTS2, direct folded proteins to the peroxisomal matrix. Montilla-Martinez et al. (2015) identify a PTS2-specific pore, which contains the PTS2 co-receptor Pex18 and the Pex14/Pex17-docking complex as major constituents. The data demonstrate that import of PTS1 and PTS2 proteins is performed by distinct pores.

Highlights

Import of folded proteins into peroxisomes requires distinct
PTS-specific pores

PTS2 pore is formed by the cytosolic co-receptor Pex18 and
docking complex Pex14/Pex17

The PTS2 receptor is not part of the unloaded pore

Complex gating of the PTS2 channel is voltage and cargo
dependent

SUMMARY

Two peroxisomal targeting signals, PTS1 and PTS2, recognized by cytosolic receptors Pex5 and cooperating Pex7/Pex18, direct folded proteins to the peroxisomal matrix. A pore consisting of the PTS1 receptor Pex5 and the docking protein Pex14 imports PTS1 proteins. We identified a distinct PTS2-specific pore, which contains the PTS2 co-receptor Pex18 and the Pex14/Pex17-docking complex asmajor constituents. The estimated maximal pore size of 4.7 nm is large enough to allow import of folded PTS2 proteins. PTS2 cargo proteins modulate complex gating, open probability, and subconductance states of the pore. While the PTS1 channel is transiently activated by arriving receptor-cargo complexes, the reconstituted PTS2 channel is constitutively present in an open state. However, the cargo-loaded PTS2 channel is largely impermeable to solutes and ions. Our results demonstrate that import of PTS1 and PTS2 proteins does not converge at the peroxisomal membrane as previously anticipated but is performed by distinct pores.

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A maquinaria de importação proteica peroxissomal: mero acaso, fortuita necessidade ou design inteligente?

FEBS Letters
Volume 581, Issue 15, 19 June 2007, Pages 2811–2819
Vienna Special Issue: Molecular Machines

Minireview

The peroxisomal protein import machinery

Edited by Horst Feldmann

Harald W. Platta, Ralf Erdmann

Abteilung für Systembiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum, Germany

Received 2 March 2007, Revised 27 March 2007, Accepted 2 April 2007, Available online 9 April 2007

Under an Elsevier user license

Peroxisomal matrix protein import cascade. The peroxisomal protein import conceptually can be divided in four steps: (i) cargo recognition in the cytosol and direction of the receptor–cargo complexes to the peroxisomal membrane. (ii) Translocation of the receptor–cargo complex to the luminal site of the peroxisomal membrane. (iii) Disassembly of the receptor–cargo complex in the peroxisomal lumen and (iv) return of the receptor to the cytosol.

Abstract

Peroxisomes are unique organelles whose physiological functions vary depending on the cellular environment or metabolic and developmental state of the organism. These changes in enzyme content are accomplished by the dynamically operating membrane and matrix protein import machineries of peroxisomes that rely on the concerted function of at least 20 peroxins. The import of folded matrix proteins is mediated by cycling receptors that shuttle between the cytosol and peroxisomal lumen. Receptor release back to the cytosol represents the ATP-dependent step of peroxisomal matrix protein import, which consists of two energy-consuming reactions: receptor ubiquitination and dislocation.

Abbreviations

AAA, ATPase associated with various cellular activities; ERAD, endoplasmatic reticulum associated degradation; PTS, peroxisomal targeting signal; RING, really interesting new gene; Ub, ubiquitin

Keywords

Peroxisome biogenesis; Protein targeting; PEX; Peroxin; Ubiquitination; AAA ATPases

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O genoma do tardígrado H. dujardini como novo modelo no estudo da evolução do desenvolvimento

quarta-feira, dezembro 02, 2015

The tardigrade Hypsibius dujardini, a new model for studying the evolution of development

Willow N. Gabriel a, Robert McNuff b, Sapna K. Patel a, T. Ryan Gregory c, William R. Jeck a, Corbin D. Jones a, Bob Goldstein a.



Abstract

Studying development in diverse taxa can address a central issue in evolutionary biology: how morphological diversity arises through the evolution of developmental mechanisms. Two of the best-studied developmental model organisms, the arthropod Drosophila and the nematode Caenorhabditis elegans, have been found to belong to a single protostome superclade, the Ecdysozoa. This finding suggests that a closely related ecdysozoan phylum could serve as a valuable model for studying how developmental mechanisms evolve in ways that can produce diverse body plans. Tardigrades, also called water bears, make up a phylum of microscopic ecdysozoan animals. Tardigrades share many characteristics with C. elegans and Drosophila that could make them useful laboratory models, but long-term culturing of tardigrades historically has been a challenge, and there have been few studies of tardigrade development. Here, we show that the tardigrade Hypsibius dujardini can be cultured continuously for decades and can be cryopreserved. We report that H. dujardini has a compact genome, a little smaller than that of C. elegans or Drosophila, and that sequence evolution has occurred at a typical rate. H. dujardini has a short generation time, 13–14 days at room temperature. We have found that the embryos of H. dujardini have a stereotyped cleavage pattern with asymmetric cell divisions, nuclear migrations, and cell migrations occurring in reproducible patterns. We present a cell lineage of the early embryo and an embryonic staging series. We expect that these data can serve as a platform for using H. dujardini as a model for studying the evolution of developmental mechanisms.

Keywords: Development; Evolution; Ecdysozoa; Tardigrade; Lineage; Model system

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O genoma do tardígrado (urso da água) Hypsibius dujardini

The genome of the tardigrade Hypsibius dujardini

Georgios Koutsovoulos, Sujai Kumar, Dominik R Laetsch, Lewis Stevens, Jennifer Daub, Claire Conlon, Habib Maroon, Fran Thomas, Aziz Aboobaker, Mark Blaxter

doi: http://dx.doi.org/10.1101/033464


Abstract

Tardigrades are meiofaunal ecdysozoans and are key to understanding the origins of Arthropoda. We present the genome of the tardigrade Hypsibius dujardini, assembled from Illumina paired and mate-pair data. While the raw data indicated extensive contamination with bacteria, presumably from the gut or surface of the animals, careful cleaning generated a clean tardigrade dataset for assembly. We also generated an expressed sequence tag dataset, a Sanger genome survey dataset and used these and Illumina RNA-Seq data for assembly validation and gene prediction. The genome assembly is ~130 Mb in span, has an N50 length of over 50 kb, and an N90 length of 6 kb. We predict 23,031 protein-coding genes in the genome, which is available in a dedicated genome browser at http://www.tardigrades.org. We compare our assembly to a recently published one for the same species and do not find support for massive horizontal gene transfer. Additional analyses of the genome are ongoing.

Copyright 

The copyright holder for this preprint is the author/funder. It is made available under a CC-BY 4.0 International license.

FREE PDF GRATIS: bioRxiv

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Vide pesquisa publicada antes no PNAS, afirmando a extensa transferência horizontal de gene:

Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade

Thomas C. Boothby et al.

Quem está certo? Boothby et al ou Koutsovoulos et al???

A árvore do sexo: processos evolucionários e ecológicos

Tree of Sex - a database of eukaryotic sex determination systems…



Sex is universal among living organisms, yet a mind-boggling diversity of mechanisms that determine the sex of an individual exists. These include chromosomal sex determination (such as in humans, where males have an X and a Y chromosome, and females have two X chromosomes), environmental sex determination (such as in many reptiles, where environmental cues – such as temperature – determine sex), or haplo-diploid sex determination (where fertilized eggs develop as females, and unfertilized eggs develop as males – such as in bees), amongst others. While some taxonomic groups (such as mammals and birds) have stable sex determination mechanisms, in other taxa (such as insects and fish), sex determination mechanisms can vary greatly among closely related species, or even among individuals within a species.


This variation is surprising, given that sex determination is a fundamental biological process. The evolutionary forces that drive this variation of sex determination systems are not understood. The “Tree of Sex Consortium” has assembled a database which is listing sexual systems and sex determination mechanisms across the eukaryotic tree of life. By synthesizing existing data on sexual systems, the database allows biologists to identify the evolutionary and ecological processes that underlie the remarkable diversity in sexual systems across the tree of eukaryotic life.

A história do ribossomo e a origem da tradução

History of the ribosome and the origin of translation

Anton S. Petrov a,1, Burak Gulen a, Ashlyn M. Norris a, Nicholas A. Kovacs a, Chad R. Bernier a, Kathryn A. Lanier a, George E. Fox b, Stephen C. Harvey c, Roger M. Wartell c, Nicholas V. Hud a, and Loren Dean Williams a,1

aSchool of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332;

bDepartment of Biology and Biochemistry, University of Houston, Houston, TX, 77204;

cSchool of Biology, Georgia Institute of Technology, Atlanta, GA 30332

Edited by David M. Hillis, The University of Texas at Austin, Austin, TX, and approved November 6, 2015 (received for review May 18, 2015)


Significance

The ribosome, in analogy with a tree, contains a record of its history, spanning 4 billion years of life on earth. The information contained within ribosomes connects us to the prehistory of biology. Details of ribosomal RNA variation, observed by comparing three-dimensional structures of ribosomes across the tree of life, form the basis of our molecular-level model of the origins and evolution of the translational system. We infer many steps in the evolution of translation, mapping out acquisition of structure and function, revealing much about how modern biology originated from ancestral chemical systems.

Abstract

We present a molecular-level model for the origin and evolution of the translation system, using a 3D comparative method. In this model, the ribosome evolved by accretion, recursively adding expansion segments, iteratively growing, subsuming, and freezing the rRNA. Functions of expansion segments in the ancestral ribosome are assigned by correspondence with their functions in the extant ribosome. The model explains the evolution of the large ribosomal subunit, the small ribosomal subunit, tRNA, and mRNA. Prokaryotic ribosomes evolved in six phases, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization. Two additional phases exclusive to eukaryotes led to tentacle-like rRNA expansions. In this model, ribosomal proteinization was a driving force for the broad adoption of proteins in other biological processes. The exit tunnel was clearly a central theme of all phases of ribosomal evolution and was continuously extended and rigidified. In the primitive noncoding ribosome, proto-mRNA and the small ribosomal subunit acted as cofactors, positioning the activated ends of tRNAs within the peptidyl transferase center. This association linked the evolution of the large and small ribosomal subunits, proto-mRNA, and tRNA.

RNA evolution translation origin of life A-minor interactions

Footnotes

1To whom correspondence may be addressed. 

Email: anton.petrov{at}biology.gatech.edu or 

loren.williams{at}chemistry.gatech.edu.

Author contributions: A.S.P., C.R.B., G.E.F., S.C.H., R.M.W., N.V.H., and L.D.W. designed research; A.S.P., B.G., A.M.N., N.A.K., and K.A.L. performed research; C.R.B. contributed new reagents/analytic tools; A.S.P., B.G., A.M.N., N.A.K., C.R.B., and K.A.L. analyzed data; A.S.P. and B.G. prepared the figures; and A.S.P., G.E.F., S.C.H., R.M.W., N.V.H., and L.D.W. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1509761112/-/DCSupplemental.

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Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao Portal de Periódicos CAPES/MEC podem ler gratuitamente este artigo do PNAS e de mais 30.000 publicações científicas.

As esponjas são realmente o filo animal mais antigo

Genomic data do not support comb jellies as the sister group to all other animals

Davide Pisani a,b,1, Walker Pett c, Martin Dohrmann d, Roberto Feuda e, Omar Rota-Stabelli f, Hervé Philippe g,h, Nicolas Lartillot c, and Gert Wörheide d,i,1

aSchool of Earth Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom;

bSchool of Biological Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom;

cLaboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France;

dDepartment of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany;

eDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;

fDepartment of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’ Adige 38010, Italy;

gCentre for Biodiversity Theory and Modelling, USR CNRS 2936, Station d’Ecologie Expérimentale du CNRS, Moulis 09200, France;

hDépartement de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montreal, QC, Canada H3C 3J7;

iBayerische Staatssammlung für Paläontologie und Geologie, Munich 80333, Germany

Edited by Neil H. Shubin, The University of Chicago, Chicago, IL, and approved November 2, 2015 (received for review September 11, 2015)

Sponge - Red Sea - Gert Wörheid

Significance

Clarifying the phylogeny of animals is fundamental to understanding their evolution. Traditionally, sponges have been considered the sister group of all other extant animals, but recent genomic studies have suggested comb jellies occupy that position instead. Here, we analyzed the current genomic evidence from comb jellies and found no convincing support for this hypothesis. Instead, when analyzed with appropriate methods, recent genomic data support the traditional hypothesis. We conclude that the alternative scenario of animal evolution according to which ctenophores evolved morphological complexity independently from cnidarians and bilaterians or, alternatively, sponges secondarily lost a nervous system, muscles, and other characters, is not supported by the available evidence.

Abstract

Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the “Ctenophora-sister” hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.

Metazoa Ctenophora Porifera phylogenomics evolution

Footnotes

1To whom correspondence may be addressed. Email: davide.pisani{at}bristol.ac.uk or woerheide{at}lmu.de.

Author contributions: D.P. and G.W. designed research; D.P., W.P., and M.D. performed research; W.P., N.L., and G.W. contributed new reagents/analytic tools; D.P., W.P., M.D., R.F., O.R.-S., H.P., N.L., and G.W. analyzed data; D.P., W.P., M.D., R.F., O.R.-S., H.P., N.L., and G.W. wrote the paper; and R.F., O.R.-S., and G.W. created the figures.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: The scripts to run our gene content analyses have been deposited in Github, github.com/willpett/ctenophora-gene-content (apart from implementing the methods in MrBayes).

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1518127112/-/DCSupplemental.

Freely available online through the PNAS open access option.

FREE PDF GRATIS: PNAS

Os pêssegos precederam aos humanos: evidência fóssil do sudoeste da China

Peaches Preceded Humans: Fossil Evidence from SW China

Tao Su, Peter Wilf, Yongjiang Huang, Shitao Zhang & Zhekun Zhou

Scientific Reports 5, Article number: 16794 (2015)

doi:10.1038/srep16794

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Received: 05 May 2015
Accepted: 16 October 2015
Published online: 26 November 2015

Evolution | Palaeontology

Altmetric: 131More detail

Article | OPEN

Peaches Preceded Humans: Fossil Evidence from SW China

Tao Su, Peter Wilf, Yongjiang Huang, Shitao Zhang & Zhekun Zhou

Scientific Reports 5, Article number: 16794 (2015)
doi:10.1038/srep16794


Abstract

Peach (Prunus persica, Rosaceae) is an extremely popular tree fruit worldwide, with an annual production near 20 million tons. Peach is widely thought to have origins in China, but its evolutionary history is largely unknown. The oldest evidence for the peach has been Chinese archaeological records dating to 8000–7000 BP. Here, we report eight fossil peach endocarps from late Pliocene strata of Kunming City, Yunnan, southwestern China. The fossils are identical to modern peach endocarps, including size comparable to smaller modern varieties, a single seed, a deep dorsal groove, and presence of deep pits and furrows. These fossils show that China has been a critical region for peach evolution since long before human presence, much less agriculture. Peaches evolved their modern morphology under natural selection, presumably involving large, frugivorous mammals such as primates. Much later, peach size and variety increased through domestication and breeding.

FREE PDF GRATIS: Scientific Reports

Vasos sanguíneos detectados por espectrometria de massa em fóssil de dinossauro de 80 milhões de anos

terça-feira, dezembro 01, 2015

Mass Spectrometry and Antibody-Based Characterization of Blood Vessels from Brachylophosaurus canadensis

Timothy P. Cleland*†, Elena R. Schroeter‡, Leonid Zamdborg§, Wenxia Zheng‡, Ji Eun Lee§∥, John C. Tran⊥, Marshall Bern#, Michael B. Duncan∇○, Valerie S. Lebleu∇○◆, Dorothy R. Ahlf⊥, Paul M. Thomas⊥, Raghu Kalluri∇○◆¶, Neil L. Kelleher⊥, and Mary H. Schweitzer‡□

†Marine, Earth and Atmospheric Sciences, ‡Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States

§ Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States

∥ Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea

⊥ Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States

# Protein Metrics, San Carlos, California 94070, United States

∇ Division of Matrix Biology, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, United States

○ Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States

◆ Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States

¶ Department of Biological Chemistry and Molecular Pharmacology and Harvard-MIT Division of Health Sciences and Technology, Harvard University, Cambridge, Massachusetts 02139, United States

□ North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, United States

J. Proteome Res., Article ASAP

DOI: 10.1021/acs.jproteome.5b00675

Publication Date (Web): November 23, 2015

Copyright © 2015 American Chemical Society

*E-mail: tpcleland@utexas.edu. Phone: +1-919-515-7838.

Abstract

Structures similar to blood vessels in location, morphology, flexibility, and transparency have been recovered after demineralization of multiple dinosaur cortical bone fragments from multiple specimens, some of which are as old as 80 Ma. These structures were hypothesized to be either endogenous to the bone (i.e., of vascular origin) or the result of biofilm colonizing the empty osteonal network after degradation of original organic components. Here, we test the hypothesis that these structures are endogenous and thus retain proteins in common with extant archosaur blood vessels that can be detected with high-resolution mass spectrometry and confirmed by immunofluorescence. Two lines of evidence support this hypothesis. First, peptide sequencing of Brachylophosaurus canadensis blood vessel extracts is consistent with peptides comprising extant archosaurian blood vessels and is not consistent with a bacterial, cellular slime mold, or fungal origin. Second, proteins identified by mass spectrometry can be localized to the tissues using antibodies specific to these proteins, validating their identity. Data are available via ProteomeXchange with identifier PXD001738.

Keywords: Brachylophosaurus canadensis; blood vessels; dinosaur; cytoskeleton; actin; tubulin; myosin; tropomyosin; taphonomy; preservation

Subscription or payment needed/Requer assinatura ou pagamento: Journal of Proteome Research

Luiz Felipe Pondé e a influência do darwinismo na sociedade


Luiz Felipe Pondé nos agraciará com sua explanação sobre o darwinismo e a sua influência na sociedade. É nesse sábado, 5 de dezembro de 2015, às 8:00 (da manhã). Venha assistir. 

Maiores informações e inscrições aqui.