Category Archives: Cell and molecular biology

Cell and molecular biology

Eran Segal

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Weizmann Institute of Science, Rehovot, Israel

A computational biologist looks at how identical cells come to differ.

My main interest is in understanding how complex biological behaviours are encoded by DNA. An example of such behaviour is the ability of genetically identical cells to generate diversity in their phenotypes, or observable traits, by changing how genes are expressed from one cell to the next. How expression variability occurs over short timescales (for example, during a cell cycle) has been well studied; much less is known about it over longer timescales.

So I was excited by work from Narendra Maheshri of the Massachusetts Institute of Technology in Cambridge and his colleagues. They demonstrate that slow expression fluctuations of a yeast gene are regulated locally, or in cis, by that gene’s promoter — a nearby stretch of DNA that regulates the gene’s expression (L. M. Octavio et al. PLoS Genet. 5, e1000673; 2009).

They studied the yeast protein FLO11, placing two copies of the protein’s promoter in the same cell, each in front of an engineered fluorescent ‘reporter’ gene. The reporters switched expression slowly and independently, implying that the expression fluctuations were locally encoded. The authors further identified global, or trans, regulators that affect the fast and slow expression fluctuations of FLO11. The type of expression effect that a regulator exerts seems to depend on several factors, including the location of the regulator relative to the site at which transcription, or reading of the DNA, begins, and relative to sites for other regulators.

Although the mechanistic details of this encoding are still unclear, applying similar approaches to many more promoters should bring us closer to understanding how other complex phenomena are encoded by DNA. This will hopefully allow us to one day predict the phenotypic effects of human genetic variation.

Viola Vogel

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Swiss Federal Institute of Technology, Zurich

A bioengineer discusses how mechanical forces in tissues may promote malignancy.

The connective-tissue protein collagen has been considered to be a structural barrier against tumour invasion in tissues. Enzymes that cleave collagen and other extracellular matrix (ECM) molecules were thus thought to promote tumour progression, but inhibitors of these enzymes have failed in clinical trials. And paradoxically, increased collagen expression is associated with a greater incidence of cancer spread.

Working with mice, Valerie Weaver of the University of California, San Francisco, and her team show that other ECM-remodelling parameters regulate malignancy (K. R. Levental et al. Cell 139, 891–906; 2009). They studied an enzyme that initiates collagen crosslinking and is often found in tissue around tumours. They reveal that the crosslinking increases the stiffness of collagen matrices, which upregulates growth-factor signalling and breast malignancy. This suggests that tumour progression depends on a tissue-remodelling process that is regulated by biochemical and mechanical factors.

Bioengineers developing implantable materials that promote tissue regeneration can also learn a lot from this paper. Dense collagen capsules typically form around implanted biomaterials, which has prompted a search for clues to how to engineer surfaces that promote blood-vessel formation and tissue regeneration rather than scarring.

Knowing which factors promote malignancy may also help us to engineer materials and tissues that tip the balance towards enhanced tissue regeneration. This paper might thus stimulate ideas on how to interfere with the interplay between ECM-crosslinking enzymes that enhance matrix stiffness and ECM-protein-cleaving enzymes. Doing so may affect mechanosensitive cell-signalling pathways, promoting regeneration.

Jay Shendure

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University of Washington, Seattle

A geneticist discusses a way to assess the effects of disease-causing gene mutations.

Although thousands of rare inherited disorders are clearly monogenic — caused by single-gene mutations — the overall picture is usually more complex. Genetic and environmental modifiers, as well as differences in the gene variants themselves, can affect how disease genes are expressed and how a disease manifests itself (the phenotype).

Marc Vidal of the Dana-Farber Cancer Institute in Boston, Massachusetts, and his team reveal that disease-causing mutations may fit into two groups on the basis of the type of perturbation they cause. ‘Edgetic’ mutations affect specific interactions in a network of genes, whereas ‘nodal’ ones remove proteins from the network altogether (Q. Zhong et al. Mol. Sys. Biol. 5, 321; 2009). The researchers did computational analyses, using the tendency of disease-associated mutations to be in-frame — producing full-length mutated proteins — or truncating, producing truncated proteins, as a proxy for edgetic or nodal perturbations, respectively. They found that, for many genes underlying multiple diseases, different phenotypes were associated with different ratios of in-frame versus truncating mutations.

The authors then did experiments evaluating whether disease-associated mutations tend to disrupt known protein–protein interactions in a way that is consistent with edgetic versus nodal perturbation. They suggest that at least some of the phenotypic variability in monogenic diseases might correlate with specific patterns of network perturbation.

The experiments are limited, but the approach of cloning mutations and serially evaluating their impact is appealing. Various genome-sequencing projects will soon catalogue hundreds of thousands of coding variants of uncertain significance. Generalized, scalable methods to evaluate the functional relevance of these variants and to place them into a broader biological context will be crucial.

Monica Gotta

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University of Geneva Medical School, Switzerland

A cell biologist connects her research to bacterial brain invasion.

My main interest is in understanding how some cells organize their structure and components asymmetrically — a property called cell polarity. When I moved to my current job in a medical faculty I was asked to teach a course on infectious diseases. So I was very excited by the publication of a paper from Mathieu Coureuil at the University of Paris Descartes and his colleagues that brings together my passion and my teaching activity. The work shows that a bacterial pathogen can reach the brain by destroying cell polarity (Coureuil, M. et al. Science 325, 83–87; 2009).

Few bacteria are able to cross the blood–brain barrier, and it is not known whether those that can do so by moving through or between cells. The bacterium Neisseria meningitidis can cross this barrier. It adheres to cells lining the brain’s blood vessels using type IV pili — hairlike appendages that connect the bacterium to the interior of these endothelial cells.

Using human brain endothelial cells and N. meningitidis in culture, Coureuil et al. show that a complex of polarity proteins — Cdc42, PAR6, PKC and PAR3, which form tight junctions between endothelial cells — are recruited to the site of bacterial adhesion. This results in depletion of these proteins at the junctions and thus the formation of gaps between infected cells.

Although this study was performed in cultured cells owing to a lack of suitable animal models, it strongly suggests that N. meningitidis enters the brain by disrupting the junctions between cells — allowing the bacteria to squeeze in between them — and not by penetrating the cells themselves.

This elegant paper unveils a route that may also be used by other pathogens that cross the blood–brain barrier. It also underscores an important function of cell polarity: protecting our brain from infectious diseases.

Reuben Shaw

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The Salk Institute for Biological Studies, La Jolla, California

A cancer researcher ponders a fundamental connection between nutrients and gene expression.

Nutrient availability to single-celled organisms varies according to their environment, and proteins in the cell that sense nutrient levels alter gene expression to increase uptake and use of specific metabolites to fuel cellular processes. Conversely, most cells in multicellular organisms are exposed to constant nutrient levels by the bloodstream, and so far there are few examples of metabolism being directly coupled to the control of gene expression.

A recent paper by Craig Thompson and his colleagues at the University of Pennsylvania in Philadelphia uncovers a direct connection between a well-known metabolic enzyme — ATP citrate lyase (ACL) — and changes in gene expression (K. E. Wellen et al. Science 324, 1076–1080; 2009). Through a chain of reactions, ACL influences the functioning of the histones, proteins that package lengths of DNA — and unpackage them for ‘reading’. This means that there is a basic — and surprising — relationship between cell glucose levels and gene expression.

We don’t yet know how metabolic challenges — for example, fasting — in whole organisms affect ACL levels or activity. But we do know that some of the same proteins that increase tumour growth also modify ACL by attaching phosphorus.

It is likely that we are just at the tip of the iceberg in terms of our understanding of the molecular basis of how metabolic inputs dictate gene-expression changes in mammalian cells. Future studies using genetic models of ACL loss in distinct mouse tissues, as well as chemical inhibitors of the enzyme, will help to elucidate in which contexts it is critical for gene-expression changes in the whole organism. Moreover, our knowledge of this metabolic linchpin may provide a therapeutic window for the treatment of certain forms of cancer, almost all of which undergo metabolic adaptation.

Peter Baumann

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Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, Missouri

A molecular biologist explores ways to revolutionize agriculture.

The complete absence of sex in a few species has long fascinated biologists, but their research is driven by more than just curiosity. Hybrid plants are the mainstay of agriculture, but require ongoing breeding and selection to maintain their desirable traits. Apomixis, or asexual reproduction by seeds, is rare among commercially important crops, but engineering plants capable of this could produce stable crops with valuable traits.

Three Herculean tasks are involved: alteration of meiosis (the cell division that normally reduces the number of chromosomes in the sex cells, or gametes) to maintain the full maternal genome; fertilization-independent development of the embryo; and formation of the endosperm tissue that nourishes the embryo.

Raphaël Mercier of the French National Institute for Agricultural Research in Versailles and his team have taken a step towards achieving this goal. Using a combination of three mutants, they engineered a mustard weed that produces gametes carrying the complete maternal genome (I. d’Erfurth et al. PLoS Biol. 7, e1000124; 2009). Their breakthrough came while characterizing a mutation in the aptly named omission of second division (osd1) gene, which causes the reproductive cells to skip the second meiotic division. By combining an osd1 mutant with mutations that modify two other steps in meiosis, the team made meiosis similar to mitosis — cell division that occurs in non-reproductive cells.

Conservation of the genes involved across crop species fosters hopes that the strategy can be applied to many of them. The problem of endosperm formation will have to be overcome, and unfertilized seeds will need to be coaxed into development. The available tool kit of mutants affecting these processes makes me optimistic that these challenges will be overcome. However, convincing consumers that heavily engineered plants can secure future food supplies may require more than scientific ingenuity.

Robert Blelloch

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University of California, San Francisco

A computational biologist looks at how mRNA length changes during development.

I am always amazed by how we start as a fertilized egg and develop into a complex, multicellular organism. This feat occurs despite the fact that the DNA in every cell — even the most specialized ones — remains, for the most part, unchanged.

One method of regulating gene activity in differentiated, or specialized, cells is through the messenger RNA (mRNA), the code of which is translated to make proteins. For example, proteins and other RNAs can bind to the untranslated regions (UTRs) at the 5’ and 3’ ends of mRNAs to regulate mRNA stability and translation.

The constitution of the 3’ UTR itself can be regulated through alternative polyadenylation, whereby one of several possible UTR sites is cleaved, followed by the addition of adenosine-based molecules to its end. A broad shift in cleavage site choice — and thus 3’ UTR length — during mammalian development was recently described by Bin Tian and his team at the University of Medicine and Dentistry of New Jersey in Newark (Z. Ji et al. Proc. Natl Acad. Sci. USA 106, 7028–7033; 2009).

By analysing genomic data, they show that 3’ UTRs generally get longer during development and cell differentiation. The authors further show that most of the genes in which 3’ UTRs are lengthened are also those that are increasingly suppressed during differentiation, such as the genes for DNA replication and cell division.

These findings bring to the forefront an underappreciated mechanism of genetic regulation that is likely to be important for normal cell differentiation. It is fascinating how many steps of the central dogma (DNA to RNA to protein) are controlled. This seems to be how evolution has managed to take a relatively simple cell and multiply it to form the complex body plan of the human.

Jason W. Chin

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MRC Laboratory of Molecular Biology, Cambridge

A molecular biologist gets excited about making designer proteins in cells.

The genetic code describes the relationship between the heritable information in the genome and the amino acids that are strung together to make proteins. This code, like any that contains redundancy, is open to hacking, and I have long been fascinated by how the process of translation, by which cells string amino acids together, might be reprogrammed to make new polymers. Several labs have already manipulated cells to incorporate designer amino acids into their proteins.

But Peter Schultz and his colleagues at the Scripps Research Institute in La Jolla, California, have achieved something remarkable. Proteins are made from a set of 20 amino acids, each of which contains an amine and a carboxylic acid group flanking a central carbon atom. Schultz’s team engineered a bacterial cell to work with amino-acid-like molecules called -hydroxy acids that have an alcohol group where the amine would normally be. During translation, instead of forming an amide bond to link polymer subunits, this -hydroxy acid forms an ester bond (J. Guo et al. Angew. Chem. 120, 734–737; 2008).

Replacing a nitrogen and a hydrogen atom in a polymer chain with an oxygen atom might seem like a slight change, but it means that a protein can now be specifically cut at the ester bond in basic solution. Making esters from -hydroxy acids may first have been achieved with ribosomes in a test tube in the 1970s, but turning the process into a heritable, genetic property is a major advance: it takes synthetic biologists closer to creating organisms with designer codes to make new polymers.

One day soon, the creativity and skill with which chemists can make molecules will be coupled to the selective power of organismal evolution. And we will watch new life forms boot up.

Manyuan Long

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University of Chicago, Illinois, USA

An evolutionary geneticist is surprised by genes of unknown origin.

I once thought that, like us, every gene must have a mother. But recent work has identified some genes that seem to have no genetic ancestry. These ‘motherless’ genes pose a new challenge to understanding the molecular mechanisms and evolutionary forces that shape our DNA. This isn’t the first time we’ve had to revise our ideas about gene evolution.

About 40 years ago, geneticist Susumu Ohno proposed that new genes originate when an existing gene duplicates, then one of the copies evolves a new function. Working with Chuck Langley in the early 1990s, I had the luck to discover a gene in flies that added another strand to Ohno’s story. The gene, named Jingwei, is a chimaera that formed through the combination of two existing genes.

Since then, researchers have identified many other ‘new’ genes assembled from unrelated genes and mobile DNA elements. Often the sequences’ origins can be identified. When they can’t, researchers have simply assumed that subsequent evolution has masked the relationship of the gene to its ancestral sequences.

But this is unlikely to be the case for hydra, a gene found recently in Drosophila melanogaster and closely related species (S.-T. Chen et al. PLoS Genet. 3, e107; 2007). No homologous sequences are found in a species that diverged from those carrying hydra only 13 million years ago — too recently for mutations to have obscured any related sequences. This implies that hydra arose de novo.

Another group has found a further 16 de novo genes in flies, which they propose evolved from non-coding DNA (D. J. Begun et al. Genetics 176, 1131–1137; 2007 and M. T. Levine et al. Proc. Natl Acad. Sci. USA 103, 9935–9939; 2006). These genes beg further study: what initiated their formation?

Editor’s Note, the entry previously misspelled the name of the author’s institution. Nature regrets the error.

Eörs Szathmáry

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Collegium Budapest, Hungary, and The Parmenides Foundation for the Study of Thinking, Munich, Germany

A theoretical biologist recommends thought-provoking reading on the origin of translation and the genetic code.

As Francis Crick and his co-workers once noted, “the origin of protein synthesis is a notoriously difficult problem”. Our best hopes of resolving this problem begin, in my opinion, in an RNA world.

The RNA-world hypothesis holds that RNA emerged before DNA and proteins, neatly separating the origin of life from that of the genetic code and its translation. The question then becomes: how did RNA evolve to make proteins?

In a recent paper, Yuri Wolf and Eugene Koonin of the National Institutes of Health in Bethesda, Maryland, present one scenario (Biol. Direct 2, 14; 2007).

They rightly call attention to studies that suggest that protein-based aminoacyl-tRNA synthetases, which are involved in the first steps of assembling amino acids into proteins, are relatively late evolutionary inventions. This forces us to accept the idea that protein synthesis is older than such synthetases.

Before the evolution of synthetases, the only agents that could conceivably have marshalled amino acids are RNA enzymes, or ribozymes. Wolf and Koonin share my view that the recruitment of amino acids was driven by selection for enhanced catalytic activity, and that the ancestor of the large ribosomal RNA that catalyses protein synthesis in today’s cells — a molecular ‘fossil’ — was a catalyst that linked only two amino acids.

I am less happy with these authors’ suggestion of a relatively late switch from peptide-specific proto-ribosomes to those that could use an external template such as mRNA to synthesize peptides with arbitrary sequence — but they may well be right.

They lay out an evolutionary sequence that is more complete than the scenario I once proposed. I highly recommend this well-written, thought-provoking paper.