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Raynes Y, Santiago JC, Lemieux FA, Darwin L, Rand DM. Sex, tissue, and mitochondrial interactions modify the transcriptional response to rapamycin in Drosophila. BMC Genomics 2024; 25:766. [PMID: 39107687 PMCID: PMC11304892 DOI: 10.1186/s12864-024-10647-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Many common diseases exhibit uncontrolled mTOR signaling, prompting considerable interest in the therapeutic potential of mTOR inhibitors, such as rapamycin, to treat a range of conditions, including cancer, aging-related pathologies, and neurological disorders. Despite encouraging preclinical results, the success of mTOR interventions in the clinic has been limited by off-target side effects and dose-limiting toxicities. Improving clinical efficacy and mitigating side effects require a better understanding of the influence of key clinical factors, such as sex, tissue, and genomic background, on the outcomes of mTOR-targeting therapies. RESULTS We assayed gene expression with and without rapamycin exposure across three distinct body parts (head, thorax, abdomen) of D. melanogaster flies, bearing either their native melanogaster mitochondrial genome or the mitochondrial genome from a related species, D. simulans. The fully factorial RNA-seq study design revealed a large number of genes that responded to the rapamycin treatment in a sex-dependent and tissue-dependent manner, and relatively few genes with the transcriptional response to rapamycin affected by the mitochondrial background. Reanalysis of an earlier study confirmed that mitochondria can have a temporal influence on rapamycin response. CONCLUSIONS We found significant and wide-ranging effects of sex and body part, alongside a subtle, potentially time-dependent, influence of mitochondria on the transcriptional response to rapamycin. Our findings suggest a number of pathways that could be crucial for predicting potential side effects of mTOR inhibition in a particular sex or tissue. Further studies of the temporal response to rapamycin are necessary to elucidate the effects of the mitochondrial background on mTOR and its inhibition.
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Affiliation(s)
- Yevgeniy Raynes
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI, 02912, USA.
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA.
| | - John C Santiago
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Faye A Lemieux
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI, 02912, USA
| | - Leah Darwin
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI, 02912, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA
| | - David M Rand
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI, 02912, USA.
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA.
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2
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Fulton TL, Johnstone JN, Tan JJ, Balagopal K, Dedman A, Chan AY, Johnson TK, Mirth CK, Piper MDW. Transiently restricting individual amino acids protects Drosophila melanogaster against multiple stressors. Open Biol 2024; 14:240093. [PMID: 39106944 PMCID: PMC11303031 DOI: 10.1098/rsob.240093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/01/2024] [Accepted: 07/09/2024] [Indexed: 08/09/2024] Open
Abstract
Nutrition and resilience are linked, though it is not yet clear how diet confers stress resistance or the breadth of stressors that it can protect against. We have previously shown that transiently restricting an essential amino acid can protect Drosophila melanogaster against nicotine poisoning. Here, we sought to characterize the nature of this dietary-mediated protection and determine whether it was sex, amino acid and/or nicotine specific. When we compared between sexes, we found that isoleucine deprivation increases female, but not male, nicotine resistance. Surprisingly, we found that this protection afforded to females was not replicated by dietary protein restriction and was instead specific to individual amino acid restriction. To understand whether these beneficial effects of diet were specific to nicotine or were generalizable across stressors, we pre-treated flies with amino acid restriction diets and exposed them to other types of stress. We found that some of the diets that protected against nicotine also protected against oxidative and starvation stress, and improved survival following cold shock. Interestingly, we found that a diet lacking isoleucine was the only diet to protect against all these stressors. These data point to isoleucine as a critical determinant of robustness in the face of environmental challenges.
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Affiliation(s)
- Tahlia L. Fulton
- School of Biological Sciences, Monash University, Clayton, Victoria3800, Australia
| | - Joshua N. Johnstone
- School of Biological Sciences, Monash University, Clayton, Victoria3800, Australia
| | - Jing J. Tan
- School of Biological Sciences, Monash University, Clayton, Victoria3800, Australia
| | - Krithika Balagopal
- School of Biological Sciences, Monash University, Clayton, Victoria3800, Australia
| | - Amy Dedman
- School of Biological Sciences, Monash University, Clayton, Victoria3800, Australia
| | - Andrea Y. Chan
- Biomedicine Discovery Institute, Monash University, Clayton, Victoria3800, Australia
| | - Travis K. Johnson
- School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria3086, Australia
| | - Christen K. Mirth
- School of Biological Sciences, Monash University, Clayton, Victoria3800, Australia
| | - Matthew D. W. Piper
- School of Biological Sciences, Monash University, Clayton, Victoria3800, Australia
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3
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Zhong S, Pan L, Wang Z, Zeng Z. Revealing Changes in Ovarian and Hemolymphatic Metabolites Using Widely Targeted Metabolomics between Newly Emerged and Laying Queens of Honeybee ( Apis mellifera). INSECTS 2024; 15:263. [PMID: 38667393 PMCID: PMC11050517 DOI: 10.3390/insects15040263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024]
Abstract
The queen bee is a central and pivotal figure within the colony, serving as the sole fertile female responsible for its reproduction. The queen possesses an open circulatory system, with her ovaries immersed in hemolymph. A continuous and intricate transportation and interchange of substances exist between the ovaries and hemolymph of queen bees. To determine the characteristic metabolites in the hemolymph and ovary, as well as understand how their rapid metabolism contributes to the process of egg-laying by queens, we reared Apis mellifera queens from three different age groups: newly emerged queen (NEQ), newly laying queen (NLQ), and old laying queen (OLQ). Using widely targeted metabolomics, our study revealed that the laying queen (NLQ and OLQ) exhibited faster fatty acid metabolism, up-regulated expression of antioxidants, and significant depletion of amino acids compared to the NEQ. This study revealed that the levels of carnitine and antioxidants (GSH, 2-O-α-D-glucopyranosyl-L-ascorbic acid, L-ascorbic acid 2-phosphate, etc.) in the NLQ and OLQ were significantly higher compared to NEQ. However, most of the differentially expressed amino acids, such as L-tryptophan, L-tyrosine, L-aspartic acid, etc., detected in NLQ and OLQ were down-regulated compared to the NEQ. Following egg-laying, pathways in the queens change significantly, e.g., Tryptophan metabolism, Tyrosine metabolism, cAMP signaling pathway, etc. Our results suggest that carnitine and antioxidants work together to maintain the redox balance of the queen. Additionally, various amino acids are responsible for maintaining the queen's egg production.
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Affiliation(s)
- Shiqing Zhong
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China; (S.Z.); (L.P.); (Z.W.)
- Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Nanchang 330045, China
| | - Luxia Pan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China; (S.Z.); (L.P.); (Z.W.)
- Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Nanchang 330045, China
| | - Zilong Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China; (S.Z.); (L.P.); (Z.W.)
- Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Nanchang 330045, China
| | - Zhijiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China; (S.Z.); (L.P.); (Z.W.)
- Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Nanchang 330045, China
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4
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Gomez A, Gonzalez S, Oke A, Luo J, Duong JB, Esquerra RM, Zimmerman T, Capponi S, Fung JC, Nystul TG. A high-throughput method for quantifying Drosophila fecundity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587093. [PMID: 38585877 PMCID: PMC10996622 DOI: 10.1101/2024.03.27.587093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Measurements of Drosophila fecundity are used in a wide variety of studies, such as investigations of stem cell biology, nutrition, behavior, and toxicology. In addition, because fecundity assays are performed on live flies, they are suitable for longitudinal studies such as investigations of aging or prolonged chemical exposure. However, standard Drosophila fecundity assays have been difficult to perform in a high-throughput manner because experimental factors such as the physiological state of the flies and environmental cues must be carefully controlled to achieve consistent results. In addition, exposing flies to a large number of different experimental conditions (such as chemical additives in the diet) and manually counting the number of eggs laid to determine the impact on fecundity is time-consuming. We have overcome these challenges by combining a new multiwell fly culture strategy with a novel 3D-printed fly transfer device to rapidly and accurately transfer flies from one plate to another; the RoboCam, a low-cost, custom built robotic camera to capture images of the wells automatically; and an image segmentation pipeline to automatically identify and quantify eggs. We show that this method is compatible with robust and consistent egg laying throughout the assay period; and demonstrate that the automated pipeline for quantifying fecundity is very accurate (r2 = 0.98 for the correlation between the automated egg counts and the ground truth) In addition, we show that this method can be used to efficiently detect the effects on fecundity induced by dietary exposure to chemicals. Taken together, this strategy substantially increases the efficiency and reproducibility of high throughput egg laying assays that require exposing flies to multiple different media conditions.
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Affiliation(s)
- Andreana Gomez
- University of California, San Francisco, Department of Anatomy
| | - Sergio Gonzalez
- San Francisco State University, Department of Biology
- Center for Cellular Construction, San Francisco, CA
| | - Ashwini Oke
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
| | - Jiayu Luo
- San Francisco State University, Department of Biology
- Center for Cellular Construction, San Francisco, CA
| | - Johnny B Duong
- Center for Cellular Construction, San Francisco, CA
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
| | - Raymond M Esquerra
- Center for Cellular Construction, San Francisco, CA
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
| | - Thomas Zimmerman
- Center for Cellular Construction, San Francisco, CA
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
| | - Sara Capponi
- Center for Cellular Construction, San Francisco, CA
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
| | - Jennifer C Fung
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
- University of California, San Francisco EaRTH Center
| | - Todd G Nystul
- University of California, San Francisco, Department of Anatomy
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
- University of California, San Francisco EaRTH Center
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5
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Liu GY, Jouandin P, Bahng RE, Perrimon N, Sabatini DM. An evolutionary mechanism to assimilate new nutrient sensors into the mTORC1 pathway. Nat Commun 2024; 15:2517. [PMID: 38514639 PMCID: PMC10957897 DOI: 10.1038/s41467-024-46680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Animals sense and respond to nutrient availability in their environments, a task coordinated in part by the mTOR complex 1 (mTORC1) pathway. mTORC1 regulates growth in response to nutrients and, in mammals, senses specific amino acids through specialized sensors that bind the GATOR1/2 signaling hub. Given that animals can occupy diverse niches, we hypothesized that the pathway might evolve distinct sensors in different metazoan phyla. Whether such customization occurs, and how the mTORC1 pathway might capture new inputs, is unknown. Here, we identify the Drosophila melanogaster protein Unmet expectations (CG11596) as a species-restricted methionine sensor that directly binds the fly GATOR2 complex in a fashion antagonized by S-adenosylmethionine (SAM). We find that in Dipterans GATOR2 rapidly evolved the capacity to bind Unmet and to thereby repurpose a previously independent methyltransferase as a SAM sensor. Thus, the modular architecture of the mTORC1 pathway allows it to co-opt preexisting enzymes to expand its nutrient sensing capabilities, revealing a mechanism for conferring evolvability on an otherwise conserved system.
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Affiliation(s)
- Grace Y Liu
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 455 Main Street, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research and Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA, USA.
| | - Patrick Jouandin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Institut de Recherche en Cancérologie de Montpellier, Inserm U1194-UM-ICM, Campus Val d'Aurelle, Montpellier, Cedex 5, France
| | - Raymond E Bahng
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 455 Main Street, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research and Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
| | - David M Sabatini
- Institute of Organic Chemistry and Biochemistry, Flemingovo n. 2, 166 10 Praha 6, Prague, Czech Republic.
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6
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Kosakamoto H, Obata F, Kuraishi J, Aikawa H, Okada R, Johnstone JN, Onuma T, Piper MDW, Miura M. Early-adult methionine restriction reduces methionine sulfoxide and extends lifespan in Drosophila. Nat Commun 2023; 14:7832. [PMID: 38052797 DOI: 10.1038/s41467-023-43550-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
Methionine restriction (MetR) extends lifespan in various organisms, but its mechanistic understanding remains incomplete. Whether MetR during a specific period of adulthood increases lifespan is not known. In Drosophila, MetR is reported to extend lifespan only when amino acid levels are low. Here, by using an exome-matched holidic medium, we show that decreasing Met levels to 10% extends Drosophila lifespan with or without decreasing total amino acid levels. MetR during the first four weeks of adult life only robustly extends lifespan. MetR in young flies induces the expression of many longevity-related genes, including Methionine sulfoxide reductase A (MsrA), which reduces oxidatively-damaged Met. MsrA induction is foxo-dependent and persists for two weeks after cessation of the MetR diet. Loss of MsrA attenuates lifespan extension by early-adulthood MetR. Our study highlights the age-dependency of the organismal response to specific nutrients and suggests that nutrient restriction during a particular period of life is sufficient for healthspan extension.
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Affiliation(s)
- Hina Kosakamoto
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 650-0047, Japan
| | - Fumiaki Obata
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 650-0047, Japan.
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
| | - Junpei Kuraishi
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hide Aikawa
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Rina Okada
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 650-0047, Japan
| | - Joshua N Johnstone
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Taro Onuma
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 650-0047, Japan
| | - Matthew D W Piper
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Masayuki Miura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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7
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Liu GY, Jouandin P, Bahng RE, Perrimon N, Sabatini DM. An evolutionary mechanism to assimilate new nutrient sensors into the mTORC1 pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.541239. [PMID: 37292894 PMCID: PMC10245982 DOI: 10.1101/2023.05.25.541239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Animals must sense and respond to nutrient availability in their local niche. This task is coordinated in part by the mTOR complex 1 (mTORC1) pathway, which regulates growth and metabolism in response to nutrients1-5. In mammals, mTORC1 senses specific amino acids through specialized sensors that act through the upstream GATOR1/2 signaling hub6-8. To reconcile the conserved architecture of the mTORC1 pathway with the diversity of environments that animals can occupy, we hypothesized that the pathway might maintain plasticity by evolving distinct nutrient sensors in different metazoan phyla1,9,10. Whether such customization occurs-and how the mTORC1 pathway might capture new nutrient inputs-is not known. Here, we identify the Drosophila melanogaster protein Unmet expectations (Unmet, formerly CG11596) as a species-restricted nutrient sensor and trace its incorporation into the mTORC1 pathway. Upon methionine starvation, Unmet binds to the fly GATOR2 complex to inhibit dTORC1. S-adenosylmethionine (SAM), a proxy for methionine availability, directly relieves this inhibition. Unmet expression is elevated in the ovary, a methionine-sensitive niche11, and flies lacking Unmet fail to maintain the integrity of the female germline under methionine restriction. By monitoring the evolutionary history of the Unmet-GATOR2 interaction, we show that the GATOR2 complex evolved rapidly in Dipterans to recruit and repurpose an independent methyltransferase as a SAM sensor. Thus, the modular architecture of the mTORC1 pathway allows it to co-opt preexisting enzymes and expand its nutrient sensing capabilities, revealing a mechanism for conferring evolvability on an otherwise highly conserved system.
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Affiliation(s)
- Grace Y. Liu
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology; 455 Main Street, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Koch Institute for Integrative Cancer Research and Massachusetts Institute of Technology, Department of Biology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Patrick Jouandin
- Department of Genetics, Blavatnik Institute, Harvard Medical School; Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA 02115, USA
- Present address: Institut de Recherche en Cancérologie de Montpellier, Inserm U1194-UM-ICM; Campus Val d’Aurelle, F-34298 Montpellier Cedex 5, France
| | - Raymond E. Bahng
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology; 455 Main Street, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Koch Institute for Integrative Cancer Research and Massachusetts Institute of Technology, Department of Biology; 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School; Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA 02115, USA
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8
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Biosynthetic constraints on amino acid synthesis at the base of the food chain may determine their use in higher-order consumer genomes. PLoS Genet 2023; 19:e1010635. [PMID: 36780875 PMCID: PMC9956874 DOI: 10.1371/journal.pgen.1010635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 02/24/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
Dietary nutrient composition is essential for shaping important fitness traits and behaviours. Many organisms are protein limited, and for Drosophila melanogaster this limitation manifests at the level of the single most limiting essential Amino Acid (AA) in the diet. The identity of this AA and its effects on female fecundity is readily predictable by a procedure called exome matching in which the sum of AAs encoded by a consumer's exome is used to predict the relative proportion of AAs required in its diet. However, the exome matching calculation does not weight AA contributions to the overall profile by protein size or expression. Here, we update the exome matching calculation to include these weightings. Surprisingly, although nearly half of the transcriptome is differentially expressed when comparing male and female flies, we found that creating transcriptome-weighted exome matched diets for each sex did not enhance their fecundity over that supported by exome matching alone. These data indicate that while organisms may require different amounts of dietary protein across conditions, the relative proportion of the constituent AAs remains constant. Interestingly, we also found that exome matched AA profiles are generally conserved across taxa and that the composition of these profiles might be explained by energetic and elemental limitations on microbial AA synthesis. Thus, it appears that ecological constraints amongst autotrophs shape the relative proportion of AAs that are available across trophic levels and that this constrains biomass composition.
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