How Prochlorococcus bacteria use nitrogen sparingly in their proteins

Organisms use proteins to perform an enormous range of functions that are essential for life. Proteins are usually composed of 20 different kinds of amino acids that each contain between one and four nitrogen atoms. In aggregate, the nitrogen atoms that are bound in proteins typically account for a substantial fraction of the nitrogen in a cell. Many organisms obtain the nitrogen that they use to make proteins from the environment, where its availability can vary greatly. These observations prompt the question: can environmental nitrogen scarcity lead to adaptive evolution in the nitrogen content of proteins? In this issue, Gilbert & Fagan (2011) address this question in the marine cyanobacteria Prochlorococcus, examining a variety of ways in which cells might be thrifty with nitrogen when making proteins. They show that different Prochlorococcus strains vary substantially in the average nitrogen content of their encoded proteins and relate this variation to nitrogen availability in different marine habitats and to genomic base composition (GC content). They also consider biases in the nitrogen content of different kinds of proteins. In most Prochlorococcus strains, a group of proteins that are commonly induced during nitrogen stress are poor in nitrogen relative to other proteins, probably reflecting selection for reduced nitrogen content. In contrast, ribosomal proteins are nitrogen rich relative to other Prochlorococcus proteins, and tend to be down‐regulated during nitrogen limitation. This suggests the possibility that decaying ribosomal proteins act as a source of nitrogen‐rich amino acids during periods of nitrogen stress. This work contributes to our understanding of how nutrient limitation might lead to adaptive variation in the composition of proteins and signals that marine microbes hold great promise for testing hypotheses about protein elemental costs in the future.     

Signatures of nitrogen limitation in the elemental composition of the proteins involved in the metabolic apparatus

Nitrogen (N) is a fundamental component of nucleotides and amino acids and is often a limiting nutrient in natural ecosystems. Thus, study of the N content of biomolecules may establish important connections between ecology and genomics. However, while significant differences in the elemental composition of whole organisms are well documented, how the flux of nutrients in the cell has shaped the evolution of different cellular processes remains poorly understood. By examining the elemental composition of major functional classes of proteins in four multicellular eukaryotic model organisms, we find that the catabolic machinery shows substantially lower N content than the anabolic machinery and the rest of the proteome. This pattern suggests that ecological selection for N conservation specifically targets cellular components that are highly expressed in response to nutrient limitation. We propose that the RNA component of the anabolic machineries is the mechanistic force driving the elemental imbalance we found, and that RNA functions as an intracellular nutrient reservoir that is degraded and recycled during starvation periods. A comparison of the elemental composition of the anabolic and catabolic machineries in species that have experienced different levels of N limitation in their evolutionary history (animals versus plants) suggests that selection for N conservation has preferentially targeted the catabolic machineries of plants, resulting in a lower N content of the proteins involved in their catabolic processes. These findings link the composition of major cellular components to the environmental factors that trigger the activation of those components, suggesting that resource availability has constrained the atomic composition and the molecular architecture of the biotic processes that enable cells to respond to reduced nutrient availability.     

植物异源多倍体进化中基因表达的变化

多倍化是植物物种进化的主要动力,异源多倍体植物在形成早期发生着快速的基因表达变化。本文概述了异源多倍体植物中基因表达变化的特点,包括基因的沉默、激活和部分同源基因表达水平的变化,探讨了基因表达变化的分子机制和生物学意义,并对研究中的问题进行了分析和展望。     

Redox regulatory mechanisms in cellular stress responses

BACKGROUND: Reactive oxygen species are produced in a highly localized and specific pattern in biological stress responses. The present review examines the redox regulatory aspects of a number of molecular stress response mechanisms in both prokaryotes and eukaryotes. SCOPE: The present review provides examples representing both the cytoplasmic stress response, often studied as the heat shock response, as well as the stress response of the endoplasmic reticulum, known as the unfolded protein response. The examples have been selected to illustrate the variety of ways that redox signals mediate and affect stress responses. CONCLUSIONS: Redox regulatory mechanisms are intricately embedded in both the cytoplasmic and endoplasmic reticulum stress responses at multiple levels. Many different stimuli, both internal and external, activate endogenous production of reactive oxygen species as a necessary part of the intracellular communication system that activates stress responses.     

The role of prey nutritional status in governing protozoan nitrogen regeneration efficiency

Laboratory experiments were conducted to study nitrogen (N) regeneration by the heterotrophic marine dinoflagellate Oxyrrhis marina when ingesting phytoplankton prey of two different species and of two alternative carbon:nitrogen (C:N) ratios. Experiments were conducted in the presence of L-methionine sulfoximine (MSX) which acts as a glutamine synthetase inhibitor. Utilisation by phytoplankton of N regenerated by protozoans and other organisms drives secondary production in marine food webs. However, the rapid utilisation of this N by phytoplankton has previously hampered accurate assessment of the efficiency of protozoan N regeneration. This phenomenon is particularly problematic when the phytoplankton are nutrient stressed and most likely to rapidly utilise N. The use of MSX prevented significant utilisation by phytoplankton of protozoan regenerated N. Hence, by removing the normal pathway of N cycling, we were able to determine the N regeneration efficiency (NRE) of the protozoan. The results suggested that predator NRE could be explained in terms of the relative CN stoichiometry of prey and predator. Using a mathematical model we demonstrated that changing the method used to simulate the NRE of the protozoan trophic level has the potential to markedly modify the predicted dynamics of the simulated microbial food web.     

The stoichiometry of nitrogen and phosphorus spiralling in heterotrophic and autotrophic streams

1. Nutrient spiralling provides a conceptual framework and a whole‐system approach to investigate ecosystem responses to environmental changes. We use spiralling metrics to examine how the coupling of nitrogen and phosphorus uptake varies between streams dominated by either heterotrophic (i.e. bacteria‐dominated) or autotrophic (algal‐dominated) microbial communities. 2. Algae generally exhibit greater capacity to store nutrients than bacteria because of differences in cellular structures. These differences led us to hypothesise that the uptake of N and P in heterotrophic ecosystems should have reduced stoichiometric variation in response to changes in supply N : P compared to autotrophic ecosystems when assimilation dominates nutrient uptake. 3. To test this hypothesis, we used an array of serial nutrient additions in several streams in the South Fork Eel River watershed in Northern California. In one set of experiments, N and P were added alone and simultaneously in separate experiments to two small, heterotrophic streams to assess uptake rates and interactions between nutrient cycles. In a second set of experiments, N and P were added simultaneously at a range of N : P in one heterotrophic and one autotrophic stream to assess differences in uptake responses to changes in supply N : P. 4. Results of these experiments suggest two important conclusions. First, increased N supply significantly shortened P uptake lengths, while P addition had little impact on N uptake in both streams, indicating that uptake of non‐limiting nutrients is tightly coupled to the availability of the limiting element. Second, changes in P uptake and uptake ratios (U_N : U_P) with increased supply N : P supported our hypothesis that heterotrophic streams are more homeostatic in their responses to changes in nutrient supply than autotrophic streams, suggesting that physiological controls on nutrient use scale up to influence ecosystem‐scale patterns in nutrient cycling.     

Yeast as a model organism for studying the evolution of non-standard genetic codes.

During the last 30 years, a number of alterations to the standard genetic code have been uncovered both in prokaryotes and eukaryotic nuclear and mitochondrial genomes. But, the study of the evolutionary pathways and molecular mechanisms of codon identity redefinition has been largely ignored due to the assumption that non-standard genetic codes can only evolve through neutral evolutionary mechanisms and that they have no functional significance. The recent discovery of a genetic code change in the genus Candida that evolved through an ambiguous messenger RNA decoding mechanism is bringing that naive assumption to an abrupt end by showing, in a rather dramatic way, that genetic code changes have profound physiological and evolutionary consequences for the species that redefine codon identity. In this paper, the recent data on the evolution of the Candida genetic code are reviewed and an experimental framework based on forced evolution, molecular genetics and comparative and functional genomics methodologies is put forward for the study of non-standard genetic codes and genetic code ambiguity in general. Additionally, the importance of using Saccharomyces cerevisiae as a model organism for elucidating the evolutionary pathway of the Candida and other genetic code changes is emphasised.     

The genomic and physiological basis of life history variation in a butterfly metapopulation

Unravelling the mechanisms underlying variation in life history traits is of fundamental importance for our understanding of adaptation by natural selection. While progress has been made in mapping fitness-related phenotypes to genotypes, mainly in a handful of model organisms, functional genomic studies of life history adaptations are still in their infancy. In particular, despite a few notable exceptions, the genomic basis of life history variation in natural populations remains poorly understood. This is especially true for the genetic underpinnings of life history phenotypes subject to diversifying selection driven by ecological dynamics in patchy environments--as opposed to adaptations involving strong directional selection owing to major environmental changes, such as latitudinal gradients, extreme climatic events or transitions from salt to freshwater. In this issue of Molecular Ecology,Wheat et al. (2011) now make a significant leap forward by applying the tools of functional genomics to dispersal-related life history variation in a butterfly metapopulation. Using a combination of microarrays, quantitative PCR and physiological measurements, the authors uncover several metabolic and endocrine factors that likely contribute to the observed life history phenotypes. By identifying molecular candidate mechanisms of fitness variation maintained by dispersal dynamics in a heterogeneous environment,they also begin to address fascinating interactions between the levels of physiology, ecology and evolution.     

Factors influencing nitrogen and phosphorus excretion rates of fish in a shallow lake

Summary 1. Fish excretion can be an important source of nutrients in aquatic ecosystems. Nitrogen (N) and phosphorus (P) excretion rates are influenced by many factors, including fish diet, fish growth rate and fish size. However, the relative influence of these and other factors on community‐level excretion rates of fish is unknown. 2. We used bioenergetics modeling to estimate excretion rates of eight fish species in a shallow, Minnesota (U.S.A.) lake over four months in both 2004 and 2005. Excretion rates of each species were summed for community‐level N and P excretion rates, as well as the N : P ratio of excretion. We then used a model‐selection approach to assess ability of independent variables to predict excretion rates, and to identify the most parsimonious model for predicting N : P excretion ratios and P and N excretion rates at the community scale. Predictive models were comprised of the independent variables water temperature and average fish density, fish size, fish growth rate, nutrient content of fish and nutrient content of fish diets at the community scale. 3. Fish density and nutrient content of fish diets (either N or P) were the most parsimonious models for predicting both N and P excretion rates, and explained 96% and 92% of the variance in N and P excretion, respectively. Moreover, fish density and nutrient models had 1400‐fold more support for predicting N and 21‐fold more support for predicting P excretion relative to models based on fish density only. Water temperature, fish size, fish growth rates and nutrient content of fish showed little influence on excretion rates, and none of our independent variables showed a strong relationship with N : P ratios of excretion. 4. Past work has focused on the importance of fish density as a driver of fish excretion rates on a volumetric basis. However, our results indicate that volumetric excretion rates at the community scale will also change substantially in response to changes in relative abundance of fish prey or shifts in relative dominance of planktivores, benthivores, or piscivores. Changes in community‐scale excretion rates will have subsequent influences on algal abundance, water clarity, and other ecosystem characteristics.     

Abiotic stress-associated microRNAs in plants: discovery, expression analysis, and evolution

Abiotic stresses such as drought, cold, and high salinity are among the most adverse factors that affect plant growth and yield in the field. MicroRNAs are small RNA molecules that regulate gene expression in a sequence-specific manner and play an important role in plant stress response. Identifying abiotic stress-associated microRNAs and understanding their function will help develop new strategies for improvement of plant stress tolerance. Here we highlight recent advances in our understanding of abiotic stress-associated miRNAs in various plants, with focus on their discovery, expression analysis, and evolution.     

Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila

To investigate the potential importance of gene duplication in D. melanogaster accessory gland protein (Acp) gene evolution we carried out a computational analysis comparing annotated D. melanogaster Acp genes to the entire D. melanogaster genome. We found that two known Acp genes are actually members of small multigene families. Polymorphism and divergence data from these duplicated genes suggest that in at least four cases, protein divergence between D. melanogaster and D. simulans is a result of directional selection. One putative Acp revealed by our computational analysis shows evidence of a recent selective sweep in a non-African population (but not in an African population). These data support the idea that selection on reproduction-related genes may drive divergence of populations within species, and strengthen the conclusion that Acps may often be under directional selection in Drosophila.     

Changes in stoichiometric constraints on epilithon and benthic macroinvertebrates in response to slight nutrient enrichment of mountain rivers

1. To assess changes in stoichiometric constraints on stream benthos, we measured elemental composition of epilithon and benthic macroinvertebrates in intrinsically P‐limited mountain rivers, upstream and downstream of low‐level anthropogenic nutrient enrichment by effluents of municipal wastewater treatment plants. 2. While there was a broad range in the elemental composition of epilithon (C : P ratios of 200–16 500, C : N ratios of 8–280, N : P ratios of 8–535) and heptageniid mayfly scrapers (C : P ratios of 125–300, C : N ratios of 5.1–7.2, N : P ratios of 20–60), the average C : P ratio of epilithon was 10‐fold lower and the average C : N ratio twofold lower at more nutrient‐rich downstream sites. Nutrient ratios in benthic macroinvertebrates were lower than in epilithon and varied little between relatively nutrient‐poor and nutrient‐rich sites. 3. We modified the existing definition of producer‐consumer elemental imbalance to allow for variation in consumer nutrient content. We defined this ‘non‐homeostatic’ imbalance as the perpendicular distance between the producer and consumer C : P, C : N, or N : P ratios, and the 1 : 1 line. 4. At P‐limited sites, the estimated mayfly N : P recycling ratio was higher than the N : P ratio in epilithon, suggesting nutrient recycling by consumers could accentuate P‐limitation of epilithon. 5. Measuring the degree of producer–consumer nutrient imbalance may be important in predicting the magnitude of effects from nutrient enrichment and can help elucidate the causes and consequences of ecological patterns and processes in rivers.     

Genesis, effects and fates of repeats in prokaryotic genomes

DNA repeats are causes and consequences of genome plasticity. Repeats are created by intrachromosomal recombination or horizontal transfer. They are targeted by recombination processes leading to amplifications, deletions and rearrangements of genetic material. The identification and analysis of repeats in nearly 700 genomes of bacteria and archaea is facilitated by the existence of sequence data and adequate bioinformatic tools. These have revealed the immense diversity of repeats in genomes, from those created by selfish elements to the ones used for protection against selfish elements, from those arising from transient gene amplifications to the ones leading to stable duplications. Experimental works have shown that some repeats do not carry any adaptive value, while others allow functional diversification and increased expression. All repeats carry some potential to disorganize and destabilize genomes. Because recombination and selection for repeats vary between genomes, the number and types of repeats are also quite diverse and in line with ecological variables, such as host-dependent associations or population sizes, and with genetic variables, such as the recombination machinery. From an evolutionary point of view, repeats represent both opportunities and problems. We describe how repeats are created and how they can be found in genomes. We then focus on the functional and genomic consequences of repeats that dictate their fate.