As estruturas CryoEM revelam como o flagelo bacteriano gira e muda de direção: mero acaso, fortuita necessidade ou design inteligente?

quinta-feira, julho 25, 2024

CryoEM structures reveal how the bacterial flagellum rotates and switches direction

Prashant K. Singh, Pankaj Sharma, Oshri Afanzar, Margo H. Goldfarb, Elena Maklashina, Michael Eisenbach, Gary Cecchini & T. M. Iverson 

Nature Microbiology volume 9, pages1271–1281 (2024)

Structure of the MS-ring


Abstract

Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural uncertainty regarding the cytoplasmic C-ring, or ‘switch’, limits our understanding of how the motor transmits torque and direction to the flagellar rod. Here we report cryogenic electron microscopy structures for Salmonella enterica serovar typhimurium inner membrane MS-ring and C-ring in a counterclockwise pose (4.0 Å) and isolated C-ring in a clockwise pose alone (4.6 Å) and bound to a regulator (5.9 Å). Conformational differences between rotational poses include a 180° shift in FliF/FliG domains that rotates the outward-facing MotA/B binding site to inward facing. The regulator has specificity for the clockwise pose by bridging elements unique to this conformation. We used these structures to propose how the switch reverses rotation and transmits torque to the flagellum, which advances the understanding of bacterial chemotaxis and bidirectional motor rotation.

FREE PDF GRATIS: Nature Microbiology

Mais um roteiro para a síntese da vida...

quarta-feira, julho 24, 2024

A roadmap towards the synthesis of Life

10 July 2024, Version 1

Christine Kriebisch et al

Image/Imagem

Abstract

The synthesis of life from non-living matter has captivated scientists for centuries. It is a grand challenge aimed at unraveling the fundamental principles of life and leveraging its unique features, such as resilience, sustainability, and the ability to evolve. Synthetic life holds immense potential in biotechnology, medicine, and materials science. Advancements in synthetic biology, systems chemistry, and biophysics have brought us closer to achieving this ambitious goal. Researchers have successfully assembled cellular components and synthesized biomimetic hardware for synthetic cells, while chemical reaction networks have demonstrated potential for Darwinian evolution. However, numerous challenges persist, including defining terminology and objectives, interdisciplinary collaboration, and addressing ethical aspects and public concerns. Our perspective offers a roadmap toward the engineering of life based on discussions during a two-week workshop with scientists from around the globe.

Keywords

Synthesis of life self-replication open-ended evolution synthetic cell systems chemistry bottom-up synthetic biology biophysics

FREE PDF GRATIS: chemRxiv

Os paradoxos na origem da vida - Mysterium tremendum!

sábado, julho 20, 2024

Paradoxes in the Origin of Life

Origin of Life

Published: 22 January 2015

Volume 44, pages 339–343, (2014)

The “Open Questions” framework reflects an understandable frustration of many who study “origins” that much of current research into the “origins problem” seems to be no different conceptually from research formulated a half century ago by Orgel, Miller, and other heroes of modern prebiotic chemistry. Discussed here is an alternative approach to guide research into the origins of life, one that focuses on “paradoxes”, pairs of statements, both grounded in theory and observation, that (taken together) suggest that the “origins problem” cannot be solved.

A substantial amount of ink has been consumed by efforts to define life, without consensus. This motivates many of us experimentalists to consciously avoid the “definition trap”. We do so by noting that states of matter can be offered as exemplars for “not life” without controversy, as can states of matter that everyone agrees constitute “life”. The consensus fails to define the boundary between these two. Nevertheless, much productive discussion can follow without needing to identify “the” distinguishing feature that represents “the” unique difference between any pair of states offered. This is illustrated by a recent report on the limits of organic life in the Solar System, whose authors declined to demarcate the difference between life and non-life (Baross et al. 2007; Benner et al. 2004).

Of course, under the language and theory used by modern science to describe states of matter, pairs of “life” and “not-life” exemplars agreed by consensus certainly appear different, and in very many ways, no matter what those exemplars are. This means that the emergence of an indisputably living state (no matter how chosen) from any indisputably non-living state (no matter how chosen) appears to require a “lengthy pathway consisting of many stages” (Szostak 2012). It is, of course, an open question as to whether this appearance truly means that life actually can originate only via a lengthy pathway, or whether this appearance simply reflects incomplete and/or incorrect language and/or theories in these descriptions. Most of us hope that the second is the case, a hope that if realized would point to a very different solution to the “origins” problem. However unjustified this hope might be, classical research in “origins” has offered us little reason to abandon it.Footnote1

However, even if we accept the premise that the emergence of “biology” from “chemistry” necessarily involves a lengthy pathway, we must confront a bigger problem before we attempt to design experiments to re-create such a pathway in a laboratory. We are now 60 years into the modern era of prebiotic chemistry. That era has produced tens of thousands of papers attempting to define processes by which “molecules that look like biology” might arise from “molecules that do not look like biology”, find conditions where oligomers might form spontaneously from those molecules, identify constraints on pre-metabolic cycles that might deliver those molecules without leaking material into the complexity sometimes characterized as “asphalt”, or assemble ways to create chiral compounds largely free from their enantiomers. For the most part, these papers report “success” in the sense that those papers define the term.

And yet, the problem remains unsolved.

...

FREE PDF: Origins of Life and Evolution of Biospheres

LUCA, o último ancestral comum de toda a vida surgiu muito antes do que se pensava

sexta-feira, julho 12, 2024

The nature of the last universal common ancestor and its impact on the early Earth system

Edmund R. R. Moody, Sandra Álvarez-Carretero, Tara A. Mahendrarajah, James W. Clark, Holly C. Betts, Nina Dombrowski, Lénárd L. Szánthó, Richard A. Boyle, Stuart Daines, Xi Chen, Nick Lane, Ziheng Yang, Graham A. Shields, Gergely J. Szöllősi, Anja Spang, Davide Pisani, Tom A. Williams, Timothy M. Lenton & Philip C. J. Donoghue 

Nature Ecology & Evolution (2024)

An illustration showing how LUCA may have been attacked by viruses

Science Graphic Design

Abstract

The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA’s metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.

FREE PDF: Nature Ecology & Evolution Sup. Info. Peer Review File