DELAYED‐RESPONSE PHYLOGENETIC CORRELATION: AN OPTIMIZATION‐BASED METHOD TO TEST COVARIATION OF CONTINUOUS CHARACTERS

A new phylogenetic comparative method is proposed, based on mapping two continuous characters on a tree to generate data pairs for regression or correlation analysis, which resolves problems of multiple character reconstructions, phylogenetic dependence, and asynchronous responses (evolutionary lags). Data pairs are formed in two ways (tree‐down and tree‐up) by matching corresponding changes, Δx and Δy. Delayed responses (Δy occurring later in the tree than Δx) are penalized by weighting pairs using nodal or branch‐length distance between Δx and Δy; immediate (same‐node) responses are given maximum weight. All combinations of character reconstructions (or a random sample thereof) are used to find the observed range of the weighted coefficient of correlation r (or weighted slope b). This range is used as test statistic, and the null distribution is generated by randomly reallocating changes (Δx and Δy) in the topology. Unlike randomization of terminal values, this procedure complies with Generalized Monte Carlo requirements while saving considerable computation time. Phylogenetic dependence is avoided by randomization without data transformations, yielding acceptable type‐I error rates and statistical power. We show that ignoring delayed responses can lead to falsely nonsignificant results. Issues that arise from considering delayed responses based on optimization are discussed.     

Trait‐mediated apparent competition in an intraguild predator–prey system

Apparent competition is of broad interest due to its effects on community structure and potential applications in agriculture, restoration, and medicine. It is well‐established that apparent competition can result from changes in predator abundance or behavior caused by interactions with alternate prey, but no previous empirical study has demonstrated that apparent competition can also result from prey‐induced changes in predator morphology. This trait‐mediated alternative mechanism of apparent competition would expand the range of conditions under which apparent competition might occur in nature and identify new ways to generate or modify apparent competition in applied contexts. Here, as a proof of concept, we show that trait‐mediated apparent competition can arise from inducible offenses and show how it operates using experiments involving three ciliates. When it feeds on Colpidium kleini, the intraguild predator Tetrahymena vorax increases in size to the extent that it can then consume Paramecium aurelia, an even larger prey. When feeding only on bacteria, however, Tetrahymena remains smaller and is unable to consume Paramecium. This trait‐mediated indirect effect leads to the predatory exclusion of Paramecium, while Tetrahymena and Colpidium coexist. Developmental expansions such as those underlying the interactions observed in our study are not limited to ciliates, such as Tetrahymena, but occur among many diverse taxa and may have a surprising degree of influence over the structure and dynamics of food webs.     

Skin phototype: a new perspective

Cutaneous phototype is considered mainly related to cutaneous pigmentation and to the eumelanin/pheomelanin ratio, which is mostly genetically determined by the melanocortin 1 receptor (MC1R) polymorphisms. However, data in literature indicate that, in addition to stimulation of eumelanin synthesis, the MC1R signalling activates antioxidant, DNA repair and survival pathways. New emerging aspects regarding photoprotection and skin phototypes are going beyond those features connected to the melanin content in the skin. Important new findings link the MC1R to nuclear receptors activation, shedding light on new extra‐melanogenic effects dependent on the α‐melanocyte‐stimulating hormone (α‐MSH) activity and new ways through which such functions are modulated. These evidences indicate that several factors including melanin play a part in defining the basis for individual sun sensitivity, suggesting that the cutaneous phototype represents a ‘biochemical fingerprint’.     

Mainstreaming Arabs: Filmmaking as image making in tales from Arab Detroit

The documentary video, Tales from Arab Detroit, is enjoying a rare blend of critical and popular success. This essay is an attempt to explain why the video is so popular with American audiences (Arab and non‐Arab alike). Special attention is given to (1) the representational strategies the makers of Tales used to shape their video; (2) the identity politics underlying these strategies; and (3) how interpretive differences among the filmmakers culminated in a video that resembles, in unforeseen ways, the Arab community it depicts. The essay doubles as a critique of “main‐streaming,” a representational technique that dominates sympathetic portrayals of Others in American popular media. Tales, it is argued, possesses all the strengths and weaknesses of this technique.     

Discovery of the first light‐dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria

In all photosynthetic organisms, chlorophylls function as light‐absorbing photopigments allowing the efficient harvesting of light energy. Chlorophyll biosynthesis recurs in similar ways in anoxygenic phototrophic proteobacteria as well as oxygenic phototrophic cyanobacteria and plants. Here, the biocatalytic conversion of protochlorophyllide to chlorophyllide is catalysed by evolutionary and structurally distinct protochlorophyllide reductases (PORs) in anoxygenic and oxygenic phototrophs. It is commonly assumed that anoxygenic phototrophs only contain oxygen‐sensitive dark‐operative PORs (DPORs), which catalyse protochlorophyllide reduction independent of the presence of light. In contrast, oxygenic phototrophs additionally (or exclusively) possess oxygen‐insensitive but light‐dependent PORs (LPORs). Based on this observation it was suggested that light‐dependent protochlorophyllide reduction first emerged as a consequence of increased atmospheric oxygen levels caused by oxygenic photosynthesis in cyanobacteria. Here, we provide experimental evidence for the presence of an LPOR in the anoxygenic phototrophic α‐proteobacterium Dinoroseobacter shibae DFL12^T. In vitro and in vivo functional assays unequivocally prove light‐dependent protochlorophyllide reduction by this enzyme and reveal that LPORs are not restricted to cyanobacteria and plants. Sequence‐based phylogenetic analyses reconcile our findings with current hypotheses about the evolution of LPORs by suggesting that the light‐dependent enzyme of D. shibae DFL12^T might have been obtained from cyanobacteria by horizontal gene transfer.     

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

Large‐scale cancer genome sequencing has uncovered thousands of gene mutations, but distinguishing tumor driver genes from functionally neutral passenger mutations is a major challenge. We analyzed 800 cancer genomes of eight types to find single‐nucleotide variants (SNVs) that precisely target phosphorylation machinery, important in cancer development and drug targeting. Assuming that cancer‐related biological systems involve unexpectedly frequent mutations, we used novel algorithms to identify genes with significant phosphorylation‐associated SNVs (pSNVs), phospho‐mutated pathways, kinase networks, drug targets, and clinically correlated signaling modules. We highlight increased survival of patients with TP53 pSNVs, hierarchically organized cancer kinase modules, a novel pSNV in EGFR, and an immune‐related network of pSNVs that correlates with prolonged survival in ovarian cancer. Our findings include multiple actionable cancer gene candidates (FLNB, GRM1, POU2F1), protein complexes (HCF1, ASF1), and kinases (PRKCZ). This study demonstrates new ways of interpreting cancer genomes and presents new leads for cancer research.     

Evolution and plasticity: Divergence of song discrimination is faster in birds with innate song than in song learners in Neotropical passerine birds

Plasticity is often thought to accelerate trait evolution and speciation. For example, plasticity in birdsong may partially explain why clades of song learners are more diverse than related clades with innate song. This “song learning” hypothesis predicts that (1) differences in song traits evolve faster in song learners, and (2) behavioral discrimination against allopatric song (a proxy for premating reproductive isolation) evolves faster in song learners. We tested these predictions by analyzing acoustic traits and conducting playback experiments in allopatric Central American sister pairs of song learning oscines (N = 42) and nonlearning suboscines (N = 27). We found that nonlearners evolved mean acoustic differences slightly faster than did leaners, and that the mean evolutionary rate of song discrimination was 4.3 times faster in nonlearners than in learners. These unexpected results may be a consequence of significantly greater variability in song traits in song learners (by 54–79%) that requires song‐learning oscines to evolve greater absolute differences in song before achieving the same level of behavioral song discrimination as nonlearning suboscines. This points to “a downside of learning” for the evolution of species discrimination, and represents an important example of plasticity reducing the rate of evolution and diversification by increasing variability.     

Soprano singing in gibbons

Diversifications in primate vocalization, including human speech, are believed to reflect evolutionary modifications in vocal anatomy and physiology. Gibbon song is acoustically unique, comprising loud, melodious, penetrating pure tone‐like calls. In a white‐handed gibbon, Hylobates lar, the fundamental frequency (f₀) of song sounds is amplified distinctively from the higher harmonics in normal air. In a helium‐enriched atmosphere, f₀ does not shift, but it is significantly suppressed and 2f₀ is emphasized. This implies that the source is independent of the resonance filter of the supralaryngeal vocal tract (SVT) in gibbons, in contrast to musical wind instruments, in which the filter primarily determines f₀. Acoustic simulation further supported that gibbons' singing is produced analogously to professional human soprano singing, in which a precise tuning of the first formant (F₁) of the SVT to f₀ amplifies exclusively the f₀ component of the source. Thus, in gibbons, as in humans, dynamic control over the vocal tract configuration, rather than anatomical modifications, has been a dominant factor in determining call structure. The varied dynamic movements were adopted in response to unique social and ecological pressures in gibbons, allowing monogamous gibbons to produce pure‐tonal melodious songs in the dense tropical forests with poor visibility. Am J Phys Anthropol, 2012. © 2012 Wiley Periodicals, Inc.     

Transgenic cotton expressing CYP392A4 double‐stranded RNA decreases the reproductive ability of Tetranychus cinnabarinus

As a polyphagous pest, Tetranychus cinnabarinus has the ability to overcome the defense of various hosts, and causes severe losses to various economically important crops. Since the interaction between pest and host plants is a valuable clue to investigate potential ways for pest management, we intend to identify the key genes of T. cinnabarinus for its adaption on cotton, then, with RNA interference (RNAi) and transgenic technology, construct a transgenic cotton strain to interfere with this process, and evaluate the effect of this method on the management of the mites. The difference of gene expression of T. cinnabarinus was analyzed when it was transferred to a new host (from cowpea to cotton) through high‐throughput sequencing, and a number of differentially expressed genes involved in detoxification, digestion and specific processes during the development were classified. From them, a P450 gene CYP392A4 with high abundance and prominent over‐expression on the cotton was selected as a candidate. With transgenic technology, cotton plants expressing double‐stranded RNA of CYP392A4 were constructed. Feeding experiments showed that it can decrease the expression of the target gene, result in the reduction of reproductive ability of the mites, and the population of T. cinnabarinus showed an apparent fitness cost on the transgenic cotton. These results provide a new approach to restrict the development of mite population on the host. It is also a useful attempt to control piercing sucking pests through RNAi and transgenic technology.     

Production of highly bioactive resveratrol analogues pterostilbene and piceatannol in metabolically engineered grapevine cell cultures

Grapevine stilbenes, particularly trans‐resveratrol, have a demonstrated pharmacological activity. Other natural stilbenes derived from resveratrol such as pterostilbene or piceatannol, display higher oral bioavailability and bioactivity than the parent compound, but are far less abundant in natural sources. Thus, to efficiently obtain these bioactive resveratrol derivatives, there is a need to develop new bioproduction systems. Grapevine cell cultures are able to produce large amounts of easily recoverable extracellular resveratrol when elicited with methylated cyclodextrins and methyl jasmonate. We devised this system as an interesting starting point of a metabolic engineering‐based strategy to produce resveratrol derivatives using resveratrol‐converting enzymes. Constitutive expression of either Vitis vinifera resveratrol O‐methyltransferase (VvROMT) or human cytochrome P450 hydroxylase 1B1 (HsCYP1B1) led to pterostilbene or piceatannol, respectively, after the engineered cell cultures were treated with the aforementioned elicitors. Functionality of both gene products was first assessed in planta by Nicotiana benthamiana agroinfiltration assays, in which tobacco cells transiently expressed stilbene synthase and VvROMT or HsCYP1B1. Grapevine cell cultures transformed with VvROMT produced pterostilbene, which was detected in both intra‐ and extracellular compartments, at a level of micrograms per litre. Grapevine cell cultures transformed with HsCYP1B1 produced about 20 mg/L culture of piceatannol, displaying a sevenfold increase in relation to wild‐type cultures, and reaching an extracellular distribution of up to 45% of total production. The results obtained demonstrate the feasibility of this novel system for the bioproduction of natural and more bioactive resveratrol derivatives and suggest new ways for the improvement of production yields.     

The essential roles of cytidine diphosphate‐diacylglycerol synthase in bloodstream form Trypanosoma brucei

Lipid metabolism in Trypanosoma brucei, the causative agent of African sleeping sickness, differs from its human host in several fundamental ways. This has lead to the validation of a plethora of novel drug targets, giving hope of novel chemical intervention against this neglected disease. Cytidine diphosphate diacylglycerol (CDP‐DAG) is a central lipid intermediate for several pathways in both prokaryotes and eukaryotes, being produced by CDP‐DAG synthase (CDS). However, nothing is known about the single T. brucei CDS gene (Tb927.7.220/EC 2.7.7.41) or its activity. In this study we show TbCDS is functional by complementation of a non‐viable yeast CDS null strain and that it is essential in the bloodstream form of the parasite via a conditional knockout. The TbCDS conditional knockout showed morphological changes including a cell‐cycle arrest due in part to kinetoplast segregation defects. Biochemical phenotyping of TbCDS conditional knockout showed drastically altered lipid metabolism where reducing levels of phosphatidylinositol detrimentally impacted on glycoylphosphatidylinositol biosynthesis. These studies also suggest that phosphatidylglycerol synthesized via the phosphatidylglycerol‐phosphate synthase is not synthesized from CDP‐DAG, as was previously thought. TbCDS was shown to localized the ER and Golgi, probably to provide CDP‐DAG for the phosphatidylinositol synthases.     

Untangling knots between autophagic targets and candidate drugs,in cancer therapy

Autophagy is an evolutionarily conserved lysosomal mechanism implicated in a wide variety of pathological processes, such as cancer. Autophagy can be regulated by a limited number of autophagy‐related genes (Atgs) such as oncogenic Bcl‐2/Bcl‐X_L, mTORC1, Akt and PI3KCI, and tumour suppressive proteins PI3KCIII, Beclin‐1, Bif‐1, p53, DAPKs, PTEN and UVRAG, which play their crucial roles in regulating autophagy‐related cancer. As autophagy has a dual role in cancer cells, with tumour‐promoting and tumour‐suppressing properties, it has become an attractive target for a series of emerging small molecule drugs. In this review, we reveal new discoveries of related small molecules or chemical compounds that can regulate autophagic pathways and lead to pro‐death or pro‐survival autophagy, in different types of cancer. We discuss the knots between autophagic targets and candidate drugs, in the hope of shedding new light on exploiting new anti‐tumour small molecule drugs for future cancer therapy.     

Patterns of selection on Plasmodium falciparum erythrocyte‐binding antigens after the colonization of the New World

Pathogens, which have recently colonized a new host species or new populations of the same host, are interesting models for understanding how populations may evolve in response to novel environments. During its colonization of South America from Africa, Plasmodium falciparum, the main agent of malaria, has been exposed to new conditions in distinctive new human populations (Amerindian and populations of mixed origins) that likely exerted new selective pressures on the parasite's genome. Among the genes that might have experienced strong selective pressures in response to these environmental changes, the eba genes (erythrocyte‐binding antigens genes), which are involved in the invasion of the human red blood cells, constitute good candidates. In this study, we analysed, in South America, the polymorphism of three eba genes (eba‐140, eba‐175, eba‐181) and compared it to the polymorphism observed in African populations. The aim was to determine whether these genes faced selective pressures in South America distinct from what they experienced in Africa. Patterns of genetic variability of these genes were compared to the patterns observed at two housekeeping genes (adsl and serca) and 272 SNPs to separate adaptive effects from demographic effects. We show that, conversely to Africa, eba‐140 seemed to be under stronger diversifying selection in South America than eba‐175. In contrast, eba‐181 did not show any sign of departure from neutrality. These changes in the patterns of selection on the eba genes could be the consequence of changes in the host immune response, the host receptor polymorphisms and/or the ability of the parasite to silence or express differentially its invasion proteins.     

Cover Picture: Proteomics 15/2008

In this issue of Proteomics you will find the following highlighted articles: An old dog refines new tricks Old dogs are reputed to be slow learners but they can be subtle manipulators, able to induce younger dogs and gullible owners to share the food dish in their favor or choose the path they prefer. Two‐dimensional gel electrophoresis has been around for more than 25 years but “new and improved” versions continue to appear. Ericsson et al. scramble the order of several steps to get more information out of the combination of IPG/IEF and “shotgun” peptide analysis. Developed for studying mechanisms of drug resistance in small cell lung cancer, the modified protocol fractionates sonically disrupted cells into microsomes and soluble fractions before tryptic digestion and iTRAQ labeling for later quantitation. Digested samples were fractionated on narrow range immobilized pH gradient strips from which they were eluted for MALDI TOF or LC‐MS/MS analysis. Detection and identification of transmembrane proteins were dramatically improved. Ericsson, H. et al., Proteomics 2008, 8, 3008–3018. An evanescent view of a lectin micro‐array: through a glass faintly Lectins have the ability to distinguish closely‐related carbohydrate moieties attached (or not) to other molecules such as proteins, peptides, lipids, cells, etc. In some respects, they are much like antibodies, just not quite as specific. Using an array of 45 different lectins, the glycan portion of glycoproteins can be identified by its binding profile. Here, Uchiyama et al. report the improvements they have made to the reproducibility and sensitivity of the system. The binding of rhodamine‐labeled probes was detected in an evanescent field fluorescence‐based instrument that was capable of reaching, 10pM levels without having to wash off unbound probe. Depositing lectin spots with a non‐contact type printer, at the right humidity, and blocking with a non‐proteinaceous material greatly improved sensitivity. Uchiyama, N. et al., Proteomics 2008, 8, 3042–3050. The innate defense: multiplex proteomic probing The body's first line of defense against pathogen infection is the innate response. In the case of bacterial infection, it is initiated by the sensing of the universal Gram‐positive cell wall lipopolysaccharide (LPS) component by macrophages primarily (but not solely) through the Toll‐like receptor 4 (TLR4). To understand the regulation of the LPS response, Gu et al. developed a multiplex quantitative proteomic analysis procedure to follow the response of TLR4+ and TLR4? cell lines. The method of choice was amino acid‐coded mass tagging (AACT, also referred to as SILAC). It showed high efficiency of labeling (95%) which eliminated interference with quantitation by the unlabeled fraction. Using triplex labeling of lysine (13C, 15N), the authors confirmed that TLR4? cells did show a response to LPS: 25 proteins were up‐regulated in TLR4+ cells, 5 in TLR4? cells. More than 500 proteins could be quantitated. Gu, S. et al., Proteomics 2008, 8, 3061–3070.     

In this issue: Proteomics 15/2008

In this issue of Proteomics you will find the following highlighted articles: An old dog refines new tricks Old dogs are reputed to be slow learners but they can be subtle manipulators, able to induce younger dogs and gullible owners to share the food dish in their favor or choose the path they prefer. Two‐dimensional gel electrophoresis has been around for more than 25 years but “new and improved” versions continue to appear. Ericsson et al. scramble the order of several steps to get more information out of the combination of IPG/IEF and “shotgun” peptide analysis. Developed for studying mechanisms of drug resistance in small cell lung cancer, the modified protocol fractionates sonically disrupted cells into microsomes and soluble fractions before tryptic digestion and iTRAQ labeling for later quantitation. Digested samples were fractionated on narrow range immobilized pH gradient strips from which they were eluted for MALDI TOF or LC‐MS/MS analysis. Detection and identification of transmembrane proteins were dramatically improved. Ericsson, H. et al., Proteomics 2008, 8, 3008–3018. An evanescent view of a lectin micro‐array: through a glass faintly Lectins have the ability to distinguish closely‐related carbohydrate moieties attached (or not) to other molecules such as proteins, peptides, lipids, cells, etc. In some respects, they are much like antibodies, just not quite as specific. Using an array of 45 different lectins, the glycan portion of glycoproteins can be identified by its binding profile. Here, Uchiyama et al. report the improvements they have made to the reproducibility and sensitivity of the system. The binding of rhodamine‐labeled probes was detected in an evanescent field fluorescence‐based instrument that was capable of reaching, 10pM levels without having to wash off unbound probe. Depositing lectin spots with a non‐contact type printer, at the right humidity, and blocking with a non‐proteinaceous material greatly improved sensitivity. Uchiyama, N. et al., Proteomics 2008, 8, 3042–3050. The innate defense: multiplex proteomic probing The body's first line of defense against pathogen infection is the innate response. In the case of bacterial infection, it is initiated by the sensing of the universal Gram‐positive cell wall lipopolysaccharide (LPS) component by macrophages primarily (but not solely) through the Toll‐like receptor 4 (TLR4). To understand the regulation of the LPS response, Gu et al. developed a multiplex quantitative proteomic analysis procedure to follow the response of TLR4+ and TLR4? cell lines. The method of choice was amino acid‐coded mass tagging (AACT, also referred to as SILAC). It showed high efficiency of labeling (95%) which eliminated interference with quantitation by the unlabeled fraction. Using triplex labeling of lysine (13C, 15N), the authors confirmed that TLR4? cells did show a response to LPS: 25 proteins were up‐regulated in TLR4+ cells, 5 in TLR4? cells. More than 500 proteins could be quantitated. Gu, S. et al., Proteomics 2008, 8, 3061–3070.     

Inhibition of the PtdIns(5) kinase PIKfyve disrupts intracellular replication of Salmonella

3‐phosphorylated phosphoinositides (3‐PtdIns) orchestrate endocytic trafficking pathways exploited by intracellular pathogens such as Salmonella to gain entry into the cell. To infect the host, Salmonellae subvert its normal macropinocytic activity, manipulating the process to generate an intracellular replicative niche. Disruption of the PtdIns(5) kinase, PIKfyve, be it by interfering mutant, siRNA‐mediated knockdown or pharmacological means, inhibits the intracellular replication of Salmonella enterica serovar typhimurium in epithelial cells. Monitoring the dynamics of macropinocytosis by time‐lapse 3D (4D) videomicroscopy revealed a new and essential role for PI(3,5)P₂ in macropinosome‐late endosome/lysosome fusion, which is distinct from that of the small GTPase Rab7. This PI(3,5)P₂‐dependent step is required for the proper maturation of the Salmonella‐containing vacuole (SCV) through the formation of Salmonella‐induced filaments (SIFs) and for the engagement of the Salmonella pathogenicity island 2‐encoded type 3 secretion system (SPI2‐T3SS). Finally, although inhibition of PIKfyve in macrophages did inhibit Salmonella replication, it also appears to disrupt the macrophage's bactericidal response.     

‘Accelerated aging’: a primrose path to insight?

Organism envy afflicts most researchers who work on aging in mice; how frustrating it is to see the worm and fly biologists nail down milestone after milestone, citation after citation! Surely genetic trickery can produce mice that age in a comparable jiffy? Alas, our near‐total ignorance of what times the aging process makes it hard to guess what genes to tweak, if indeed aging can be mimicked a presto. Building a case that a given short‐lived mutant ages quickly is a steep and thorny path, requiring more than just plucking a symptom here and there from a list of things that sometimes go wrong in old people or old mice. The hallmark of aging is that a lot goes wrong more or less at the same time, in 2‐year‐old mice, 10‐year‐old dogs and 70‐year‐old people. Finding ways to damage one or two systems in a 6‐week or 6‐month‐old mouse is not too hard to do, but the implications of such studies for improved understanding of aging per se are at best indirect and at worst imaginary and distracting.     

All‐Printed,Stretchable Zn‐Ag2O Rechargeable Battery via Hyperelastic Binder for Self‐Powering Wearable Electronics

While several stretchable batteries utilizing either deterministic or random composite architectures have been described, none have been fabricated using inexpensive printing technologies. In this study, the authors printed a highly stretchable, zinc‐silver oxide (Zn‐Ag₂O) battery by incorporating polystyrene‐block ‐polyisoprene‐block ‐polystyrene (SIS) as a hyperelastic binder for custom‐made printable inks. The remarkable mechanical properties of the SIS binder lead to an all‐printed, stretchable Zn‐Ag₂O rechargeable battery with a ≈2.5 mA h cm^?2 reversible capacity density even after multiple iterations of 100% stretching. This battery offers the highest reversible capacity and discharge current density for intrinsically stretchable batteries reported to date. The electrochemical and mechanical properties are characterized under different strain conditions. The new stress‐enduring printable inks pave ways for further developing stretchable electronics for the wide range of wearable applications.     

The iron–sulphur protein RNase L inhibitor functions in translation termination

The iron–sulphur (Fe–S)‐containing RNase L inhibitor (Rli1) is involved in ribosomal subunit maturation, transport of both ribosomal subunits to the cytoplasm, and translation initiation through interaction with the eukaryotic initiation factor 3 (eIF3) complex. Here, we present a new function for Rli1 in translation termination. Through co‐immunoprecipitation experiments, we show that Rli1 interacts physically with the translation termination factors eukaryotic release factor 1 (eRF1)/Sup45 and eRF3/Sup35 in Saccharomyces cerevisiae. Genetic interactions were uncovered between a strain depleted for Rli1 and sup35‐21 or sup45‐2. Furthermore, we show that downregulation of RLI1 expression leads to defects in the recognition of a stop codon, as seen in mutants of other termination factors. By contrast, RLI1 overexpression partly suppresses the read‐through defects in sup45‐2. Interestingly, we find that although the Fe–S cluster is not required for the interaction of Rli1 with eRF1 or its other interacting partner, Hcr1, from the initiation complex eIF3, it is required for its activity in translation termination; an Fe–S cluster mutant of RLI1 cannot suppress the read‐through defects of sup45‐2.