1
|
Danhof HA, Lee J, Thapa A, Britton RA, Di Rienzi SC. Microbial stimulation of oxytocin release from the intestinal epithelium via secretin signaling. Gut Microbes 2023; 15:2256043. [PMID: 37698879 PMCID: PMC10498800 DOI: 10.1080/19490976.2023.2256043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/11/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023] Open
Abstract
Intestinal microbes impact the health of the intestine and organs distal to the gut. Limosilactobacillus reuteri is a human intestinal microbe that promotes normal gut transit, the anti-inflammatory immune system, wound healing, normal social behavior in mice, and prevents bone reabsorption. Oxytocin impacts these functions and oxytocin signaling is required for L. reuteri-mediated wound healing and social behavior; however, the events in the gut leading to oxytocin stimulation and beneficial effects are unknown. Here we report evolutionarily conserved oxytocin production in the intestinal epithelium through analysis of single-cell RNA-Seq datasets and imaging of human and mouse intestinal tissues. Moreover, human intestinal organoids produce oxytocin, demonstrating that the intestinal epithelium is sufficient to produce oxytocin. We find that L. reuteri facilitates oxytocin secretion from human intestinal tissue and human intestinal organoids. Finally, we demonstrate that stimulation of oxytocin secretion by L. reuteri is dependent on the gut hormone secretin, which is produced in enteroendocrine cells, while oxytocin itself is produced in enterocytes. Altogether, this work demonstrates that oxytocin is produced and secreted from enterocytes in the intestinal epithelium in response to secretin stimulated by L. reuteri. This work thereby identifies oxytocin as an intestinal hormone and provides mechanistic insight into avenues by which gut microbes promote host health.
Collapse
Affiliation(s)
- Heather A. Danhof
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Jihwan Lee
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Aanchal Thapa
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Robert A. Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Sara C. Di Rienzi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
2
|
Poplaski V, Bomidi C, Kambal A, Nguyen-Phuc H, Di Rienzi SC, Danhof HA, Zeng XL, Feagins LA, Deng N, Vilar E, McAllister F, Coarfa C, Min S, Kim HJ, Shukla R, Britton R, Estes MK, Blutt SE. Human intestinal organoids from Cronkhite-Canada syndrome patients reveal link between serotonin and proliferation. J Clin Invest 2023; 133:e166884. [PMID: 37909332 PMCID: PMC10617781 DOI: 10.1172/jci166884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 08/29/2023] [Indexed: 11/03/2023] Open
Abstract
Cronkhite-Canada Syndrome (CCS) is a rare, noninherited polyposis syndrome affecting 1 in every million individuals. Despite over 50 years of CCS cases, the etiopathogenesis and optimal treatment for CCS remains unknown due to the rarity of the disease and lack of model systems. To better understand the etiology of CCS, we generated human intestinal organoids (HIOs) from intestinal stem cells isolated from 2 patients. We discovered that CCS HIOs are highly proliferative and have increased numbers of enteroendocrine cells producing serotonin (also known as 5-hydroxytryptamine or 5HT). These features were also confirmed in patient tissue biopsies. Recombinant 5HT increased proliferation of non-CCS donor HIOs and inhibition of 5HT production in the CCS HIOs resulted in decreased proliferation, suggesting a link between local epithelial 5HT production and control of epithelial stem cell proliferation. This link was confirmed in genetically engineered HIOs with an increased number of enteroendocrine cells. This work provides a new mechanism to explain the pathogenesis of CCS and illustrates the important contribution of HIO cultures to understanding disease etiology and in the identification of novel therapies. Our work demonstrates the principle of using organoids for personalized medicine and sheds light on how intestinal hormones can play a role in intestinal epithelial proliferation.
Collapse
Affiliation(s)
- Victoria Poplaski
- Program in Translational Biology and Molecular Medicine
- Department of Molecular Virology and Microbiology, and
| | | | - Amal Kambal
- Department of Molecular Virology and Microbiology, and
| | | | - Sara C. Di Rienzi
- Department of Molecular Virology and Microbiology, and
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Heather A. Danhof
- Department of Molecular Virology and Microbiology, and
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, and
| | - Linda A. Feagins
- Department of Internal Medicine, Center for Inflammatory Bowl Diseases, The University of Texas at Austin Dell Medical School, Austin, Texas, USA
| | - Nan Deng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston Texas, USA
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston Texas, USA
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston Texas, USA
| | - Cristian Coarfa
- Dan L Duncan Comprehensive Cancer Center and
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Soyoun Min
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Hyun Jung Kim
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Richa Shukla
- Department of Medicine, Section of Gasteroenterology and Hepatology, Baylor College of Medicine, Houston, Texas, USA
| | - Robert Britton
- Department of Molecular Virology and Microbiology, and
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, and
- Department of Medicine, Section of Gasteroenterology and Hepatology, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston Texas, USA
| | | |
Collapse
|
3
|
Hoerr RE, Eng A, Payen C, Di Rienzi SC, Raghuraman MK, Dunham MJ, Brewer BJ, Friedman KL. Hotspot of de novo telomere addition stabilizes linear amplicons in yeast grown in sulfate-limiting conditions. Genetics 2023; 224:iyad010. [PMID: 36702776 PMCID: PMC10213492 DOI: 10.1093/genetics/iyad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/10/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
Evolution is driven by the accumulation of competing mutations that influence survival. A broad form of genetic variation is the amplification or deletion of DNA (≥50 bp) referred to as copy number variation (CNV). In humans, CNV may be inconsequential, contribute to minor phenotypic differences, or cause conditions such as birth defects, neurodevelopmental disorders, and cancers. To identify mechanisms that drive CNV, we monitored the experimental evolution of Saccharomyces cerevisiae populations grown under sulfate-limiting conditions. Cells with increased copy number of the gene SUL1, which encodes a primary sulfate transporter, exhibit a fitness advantage. Previously, we reported interstitial inverted triplications of SUL1 as the dominant rearrangement in a haploid population. Here, in a diploid population, we find instead that small linear fragments containing SUL1 form and are sustained over several generations. Many of the linear fragments are stabilized by de novo telomere addition within a telomere-like sequence near SUL1 (within the SNF5 gene). Using an assay that monitors telomerase action following an induced chromosome break, we show that this region acts as a hotspot of de novo telomere addition and that required sequences map to a region of <250 base pairs. Consistent with previous work showing that association of the telomere-binding protein Cdc13 with internal sequences stimulates telomerase recruitment, mutation of a four-nucleotide motif predicted to associate with Cdc13 abolishes de novo telomere addition. Our study suggests that internal telomere-like sequences that stimulate de novo telomere addition can contribute to adaptation by promoting genomic plasticity.
Collapse
Affiliation(s)
- Remington E Hoerr
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Alex Eng
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Celia Payen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- IFF, Wilmington, DE 19803, USA
| | - Sara C Di Rienzi
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - M K Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Bonita J Brewer
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Katherine L Friedman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| |
Collapse
|
4
|
Danhof HA, Lee J, Thapa A, Britton RA, Di Rienzi SC. Microbial stimulation of oxytocin release from the intestinal epithelium via secretin signaling. bioRxiv 2023:2023.03.09.531917. [PMID: 36945649 PMCID: PMC10028957 DOI: 10.1101/2023.03.09.531917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Intestinal microbes impact the health of the intestine and organs distal to the gut. Limosilactobacillus reuteri is a human intestinal microbe that promotes normal gut transit 1 , the anti-inflammatory immune system 2-4 , wound healing 5-7 , normal social behavior in mice 8-10 , and prevents bone reabsorption 11-17 . Each of these functions is impacted by oxytocin 18-22 , and oxytocin signaling is required for L. reuteri- mediated wound healing 5 and social behavior 9 ; however, the initiating events in the gut that lead to oxytocin stimulation and related beneficial functions remain unknown. Here we found evolutionarily conserved oxytocin production in the intestinal epithelium through analysis of single-cell RNA-Seq datasets and imaging of human and mouse intestinal tissues. Moreover, human intestinal organoids produce oxytocin, demonstrating that the intestinal epithelium is sufficient to produce oxytocin. We subsequently found that L. reuteri facilitates oxytocin secretion directly from human intestinal tissue and human intestinal organoids. Finally, we demonstrate that stimulation of oxytocin secretion by L. reuteri is dependent on the gut hormone secretin, which is produced in enteroendocrine cells 23 , while oxytocin itself is produced in enterocytes. Altogether, this work demonstrates that oxytocin is produced and secreted from enterocytes in the intestinal epithelium in response to secretin stimulated by L. reuteri . This work thereby identifies oxytocin as an intestinal hormone and provides mechanistic insight into avenues by which gut microbes promote host health.
Collapse
Affiliation(s)
- Heather A. Danhof
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Jihwan Lee
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Aanchal Thapa
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Rice University, Houston, Texas, USA
| | - Robert A. Britton
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Sara C. Di Rienzi
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
5
|
Di Rienzi SC, Johnson EL, Waters JL, Kennedy EA, Jacobson J, Lawrence P, Wang DH, Worgall TS, Brenna JT, Ley RE. The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil. J Nutr Biochem 2021; 97:108808. [PMID: 34186211 PMCID: PMC8585862 DOI: 10.1016/j.jnutbio.2021.108808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 10/21/2022]
Abstract
Studies in mice using germfree animals as controls for microbial colonization have shown that the gut microbiome mediates diet-induced obesity. Such studies use diets rich in saturated fat, however, Western diets in the United States America are enriched in soybean oil, composed of unsaturated fatty acids, either linoleic or oleic acid. Here, we addressed whether the microbiome is a variable in fat metabolism in mice on a soybean oil diet. We used conventionally-raised, low-germ, and germfree mice fed for 10 weeks diets either high or low in high-linoleic-acid soybean oil as the sole source of fat. Conventional and germfree mice gained relative fat weight and all mice consumed more calories on the high fat vs. low fat soybean oil diet. Plasma fatty acid levels were generally dependent on diet, with microbial colonization status affecting iso-C18:0, C20:3n-6, C14:0, and C15:0 levels. Colonization status, but not diet, impacted levels of liver sphingolipids including ceramides, sphingomyelins, and sphinganine. Our results confirm that absorbed fatty acids are mainly a reflection of the diet and that microbial colonization influences liver sphingolipid pools regardless of diet.
Collapse
Affiliation(s)
- Sara C Di Rienzi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | | | - Jillian L Waters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Elizabeth A Kennedy
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Juliet Jacobson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Peter Lawrence
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Dong Hao Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Tilla S Worgall
- Department of Pathology and Cell Biology and Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - J Thomas Brenna
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA; Dell Pediatric Research Institute, Dell Medical School, University of Texas at Austin, Austin, Texas, USA
| | - Ruth E Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA; Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.
| |
Collapse
|
6
|
Criss ZK, Bhasin N, Di Rienzi SC, Rajan A, Deans-Fielder K, Swaminathan G, Kamyabi N, Zeng XL, Doddapaneni H, Menon VK, Chakravarti D, Estrella C, Yu X, Patil K, Petrosino JF, Fleet JC, Verzi MP, Christakos S, Helmrath MA, Arimura S, DePinho RA, Britton RA, Maresso AW, Grande-Allen KJ, Blutt SE, Crawford SE, Estes MK, Ramani S, Shroyer NF. Drivers of transcriptional variance in human intestinal epithelial organoids. Physiol Genomics 2021; 53:486-508. [PMID: 34612061 DOI: 10.1152/physiolgenomics.00061.2021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human intestinal epithelial organoids (enteroids and colonoids) are tissue cultures used for understanding the physiology of the human intestinal epithelium. Here, we explored the effect on the transcriptome of common variations in culture methods, including extracellular matrix substrate, format, tissue segment, differentiation status, and patient heterogeneity. RNA-sequencing datasets from 276 experiments performed on 37 human enteroid and colonoid lines from 29 patients were aggregated from several groups in the Texas Medical Center. DESeq2 and gene set enrichment analysis (GSEA) were used to identify differentially expressed genes and enriched pathways. PERMANOVA, Pearson's correlation, and dendrogram analysis of the data originally indicated three tiers of influence of culture methods on transcriptomic variation: substrate (collagen vs. Matrigel) and format (3-D, transwell, and monolayer) had the largest effect; segment of origin (duodenum, jejunum, ileum, colon) and differentiation status had a moderate effect; and patient heterogeneity and specific experimental manipulations (e.g., pathogen infection) had the smallest effect. GSEA identified hundreds of pathways that varied between culture methods, such as IL1 cytokine signaling enriched in transwell versus monolayer cultures and E2F target genes enriched in collagen versus Matrigel cultures. The transcriptional influence of the format was furthermore validated in a synchronized experiment performed with various format-substrate combinations. Surprisingly, large differences in organoid transcriptome were driven by variations in culture methods such as format, whereas experimental manipulations such as infection had modest effects. These results show that common variations in culture conditions can have large effects on intestinal organoids and should be accounted for when designing experiments and comparing results between laboratories. Our data constitute the largest RNA-seq dataset interrogating human intestinal epithelial organoids.
Collapse
Affiliation(s)
- Zachary K Criss
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Nobel Bhasin
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Sara C Di Rienzi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Kali Deans-Fielder
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | | | | | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Vipin K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Deepavali Chakravarti
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Clarissa Estrella
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xiaomin Yu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Ketki Patil
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - James C Fleet
- Department of Nutrition Sciences, The University of Texas, Austin, Texas
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Piscataway, New Jersey
| | - Sylvia Christakos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, New Jersey
| | - Michael A Helmrath
- Department of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Sumimasa Arimura
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | | | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Noah F Shroyer
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
7
|
Ruan W, Engevik MA, Chang-Graham AL, Danhof HA, Goodwin A, Engevik KA, Shi Z, Hall A, Rienzi SCD, Venable S, Britton RA, Hyser J, Versalovic J. Enhancing responsiveness of human jejunal enteroids to host and microbial stimuli. J Physiol 2020; 598:3085-3105. [PMID: 32428244 PMCID: PMC7674265 DOI: 10.1113/jp279423] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
KEY POINTS Enteroids are a physiologically relevant model to examine the human intestine and its functions. Previously, the measurable cytokine response of human intestinal enteroids has been limited following exposure to host or microbial pro-inflammatory stimuli. Modifications to enteroid culture conditions facilitated robust human cytokine responses to pro-inflammatory stimuli. This new human enteroid culture methodology refines the ability to study microbiome:human intestinal epithelium interactions in the laboratory. ABSTRACT The intestinal epithelium is the primary interface between the host, the gut microbiome and its external environment. Since the intestinal epithelium contributes to innate immunity as a first line of defence, understanding how the epithelium responds to microbial and host stimuli is an important consideration in promoting homeostasis. Human intestinal enteroids (HIEs) are primary epithelial cell cultures that can provide insights into the biology of the intestinal epithelium and innate immune responses. One potential limitation of using HIEs for innate immune studies is the relative lack of responsiveness to factors that stimulate epithelial cytokine production. We report technical refinements, including removal of extracellular antioxidants, to facilitate enhanced cytokine responses in HIEs. Using this new method, we demonstrate that HIEs have distinct cytokine profiles in response to pro-inflammatory stimuli derived from host and microbial sources. Overall, we found that host-derived cytokines tumour necrosis factor and interleukin-1α stimulated reactive oxygen species and a large repertoire of cytokines. In contrast, microbial lipopolysaccharide, lipoteichoic acid and flagellin stimulated a limited number of cytokines and histamine did not stimulate the release of any cytokines. Importantly, HIE-secreted cytokines were functionally active, as denoted by the ability of human blood-derived neutrophil to migrate towards HIE supernatant containing interleukin-8. These findings establish that the immune responsiveness of HIEs depends on medium composition and stimuli. By refining the experimental culture medium and creating an environment conducive to epithelial cytokine responses by human enteroids, HIEs can facilitate exploration of many experimental questions pertaining to the role of the intestinal epithelium in innate immunity.
Collapse
Affiliation(s)
- Wenly Ruan
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Section of Gastroenterology, Hepatology, and Nutrition, Texas Children's Hospital, Houston, Texas, USA
| | - Melinda A Engevik
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | | | - Heather A Danhof
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Annie Goodwin
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Section of Gastroenterology, Hepatology, and Nutrition, Texas Children's Hospital, Houston, Texas, USA
| | - Kristen A Engevik
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Zhongcheng Shi
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Anne Hall
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Sara C Di Rienzi
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Susan Venable
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Robert A Britton
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Joseph Hyser
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| |
Collapse
|
8
|
Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector TD, Bell JT, Youngblut ND, Hewson I, Reyes A, Ley RE. Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins. Cell Host Microbe 2019; 25:261-272.e5. [PMID: 30763537 PMCID: PMC6411085 DOI: 10.1016/j.chom.2019.01.019] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/31/2018] [Accepted: 01/24/2019] [Indexed: 01/01/2023]
Abstract
The virome is one of the most variable components of the human gut microbiome. Within twin pairs, viromes have been shown to be similar for infants, but not for adults, indicating that as twins age and their environments and microbiomes diverge, so do their viromes. The degree to which the microbiome drives the vast virome diversity is unclear. Here, we examine the relationship between microbiome and virome diversity in 21 adult monozygotic twin pairs selected for high or low microbiome concordance. Viromes derived from virus-like particles are unique to each individual, are dominated by Caudovirales and Microviridae, and exhibit a small core that includes crAssphage. Microbiome-discordant twins display more dissimilar viromes compared to microbiome-concordant twins, and the richer the microbiomes, the richer the viromes. These patterns are driven by bacteriophages, not eukaryotic viruses. Collectively, these observations support a strong role of the microbiome in patterning for the virome.
Collapse
Affiliation(s)
- J Leonardo Moreno-Gallego
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Shao-Pei Chou
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sara C Di Rienzi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Julia K Goodrich
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia; Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
| |
Collapse
|
9
|
Alves da Silva AV, de Castro Oliveira SB, Di Rienzi SC, Brown-Steinke K, Dehan LM, Rood JK, Carreira VS, Le H, Maier EA, Betz KJ, Aihara E, Ley RE, Preidis GA, Shen L, Moore SR. Murine Methyl Donor Deficiency Impairs Early Growth in Association with Dysmorphic Small Intestinal Crypts and Reduced Gut Microbial Community Diversity. Curr Dev Nutr 2018. [PMCID: PMC6324351 DOI: 10.1093/cdn/nzy070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Folate and choline are essential methyl donor nutrients throughout the life span; however, the adverse effects of combined deficiency on early growth, intestinal epithelial morphology, and the gut microbiome remain only partially understood. Objectives We investigated the effects of dietary folate and choline deficiency on early growth, small intestinal (SI) epithelial architecture, and the gut microbiota of mice. To explore potential mechanisms for adverse effects on gut epithelial morphology, we also evaluated gene expression and DNA methylation in mouse intestinal epithelial organoids (enteroids) maintained in methyl donor–deficient (MDD) conditions. Methods Pregnant dams were administered 1 of 4 diets: 1) control diet (CD−), 2) an isocaloric MDD− diet, or 3) CD+ and 4) MDD+ formulations containing 1% succinylsulfathiazole to inhibit folate-producing gut bacteria. We weaned pups to their dams’ diet at 3 wk of age and monitored body weight and tail length pre- and postweaning. We measured serum folate, SI crypt morphology, and microbiota composition at 7 wk of age. Results Both MDD+ and MDD− diets impaired early ponderal and linear growth, lowered serum folate concentrations, and produced patchy areas of increased crypt depth throughout the SI. Succinylsulfathiazole increased crypt depth independently of diet. MDD or succinylsulfathiazole, alone or in combination, altered the gut microbiome, with decreased Bacteroidales and Clostridiales, increased Lactobacillales and Erysipelotrichaceae taxa, and decreased α-diversity indexes. Enteroids maintained in MDD media displayed dysmorphic crypt domains, altered expression of stem cell and secretory differentiation genes, and decreased DNA methylation of the glycosylation genes Beta-1,4-N-Acetyl-Galactosaminyltransferase-1 (B4galnt1) and Phosphoethanolamine/Phosphocholine-Phosphatase (Phospho1). Conclusion MDD impairs ponderal and linear growth in mice in association with dysmorphic SI crypts and reduced gut microbial diversity. In vitro methyl donor deficiency similarly induced dysmorphic crypts in mouse enteroids in conjunction with altered gene expression and DNA methylation.
Collapse
Affiliation(s)
- Antonio V Alves da Silva
- Instituto de Biomedicina, Universidade Federal do Ceará, Fortaleza, Brazil
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Stephanie B de Castro Oliveira
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Sara C Di Rienzi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX
| | | | - Lauren M Dehan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Jill K Rood
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Hung Le
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Elizabeth A Maier
- Instituto de Biomedicina, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Kristina J Betz
- Instituto de Biomedicina, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Eitaro Aihara
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Geoffrey A Preidis
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine Houston, TX
| | - Lanlan Shen
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Sean R Moore
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA
| |
Collapse
|
10
|
Di Rienzi SC, Jacobson J, Kennedy EA, Bell ME, Shi Q, Waters JL, Lawrence P, Brenna JT, Britton RA, Walter J, Ley RE. Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids. eLife 2018; 7:e32581. [PMID: 29580380 PMCID: PMC5902164 DOI: 10.7554/elife.32581] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/14/2018] [Indexed: 12/15/2022] Open
Abstract
Over the past century, soybean oil (SBO) consumption in the United States increased dramatically. The main SBO fatty acid, linoleic acid (18:2), inhibits in vitro the growth of lactobacilli, beneficial members of the small intestinal microbiota. Human-associated lactobacilli have declined in prevalence in Western microbiomes, but how dietary changes may have impacted their ecology is unclear. Here, we compared the in vitro and in vivo effects of 18:2 on Lactobacillus reuteri and L. johnsonii. Directed evolution in vitro in both species led to strong 18:2 resistance with mutations in genes for lipid biosynthesis, acid stress, and the cell membrane or wall. Small-intestinal Lactobacillus populations in mice were unaffected by chronic and acute 18:2 exposure, yet harbored both 18:2- sensitive and resistant strains. This work shows that extant small intestinal lactobacilli are protected from toxic dietary components via the gut environment as well as their own capacity to evolve resistance.
Collapse
Affiliation(s)
- Sara C Di Rienzi
- Department of Microbiome ScienceMax Planck Institute for Developmental BiologyTübingenGermany
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Juliet Jacobson
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Elizabeth A Kennedy
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Mary E Bell
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Qiaojuan Shi
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Jillian L Waters
- Department of Microbiome ScienceMax Planck Institute for Developmental BiologyTübingenGermany
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Peter Lawrence
- Division of Nutritional SciencesCornell UniversityIthacaUnited States
| | - J Thomas Brenna
- Division of Nutritional SciencesCornell UniversityIthacaUnited States
- Dell Pediatric Research Institute, Dell Medical SchoolUniversity of Texas at AustinAustinUnited States
| | - Robert A Britton
- Department of Molecular Virology and MicrobiologyBaylor College of MedicineHoustonUnited States
| | - Jens Walter
- Department of Agricultural, Food, and Nutritional ScienceUniversity of AlbertaEdmontonCanada
- Department of Biological SciencesUniversity of AlbertaEdmontonCanada
| | - Ruth E Ley
- Department of Microbiome ScienceMax Planck Institute for Developmental BiologyTübingenGermany
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| |
Collapse
|
11
|
Brewer BJ, Payen C, Di Rienzi SC, Higgins MM, Ong G, Dunham MJ, Raghuraman MK. Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification. PLoS Genet 2015; 11:e1005699. [PMID: 26700858 PMCID: PMC4689423 DOI: 10.1371/journal.pgen.1005699] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/03/2015] [Indexed: 01/20/2023] Open
Abstract
DNA replication errors are a major driver of evolution—from single nucleotide polymorphisms to large-scale copy number variations (CNVs). Here we test a specific replication-based model to explain the generation of interstitial, inverted triplications. While no genetic information is lost, the novel inversion junctions and increased copy number of the included sequences create the potential for adaptive phenotypes. The model—Origin-Dependent Inverted-Repeat Amplification (ODIRA)—proposes that a replication error at pre-existing short, interrupted, inverted repeats in genomic sequences generates an extrachromosomal, inverted dimeric, autonomously replicating intermediate; subsequent genomic integration of the dimer yields this class of CNV without loss of distal chromosomal sequences. We used a combination of in vitro and in vivo approaches to test the feasibility of the proposed replication error and its downstream consequences on chromosome structure in the yeast Saccharomyces cerevisiae. We show that the proposed replication error—the ligation of leading and lagging nascent strands to create “closed” forks—can occur in vitro at short, interrupted inverted repeats. The removal of molecules with two closed forks results in a hairpin-capped linear duplex that we show replicates in vivo to create an inverted, dimeric plasmid that subsequently integrates into the genome by homologous recombination, creating an inverted triplication. While other models have been proposed to explain inverted triplications and their derivatives, our model can also explain the generation of human, de novo, inverted amplicons that have a 2:1 mixture of sequences from both homologues of a single parent—a feature readily explained by a plasmid intermediate that arises from one homologue and integrates into the other homologue prior to meiosis. Our tests of key features of ODIRA lend support to this mechanism and suggest further avenues of enquiry to unravel the origins of interstitial, inverted CNVs pivotal in human health and evolution. Chromosomal aberration such as gene amplification is a common event in human diseases and is often selected during adaptation of microorganism to stress. We proposed a replication-based model to explain the formation of a particular type of genomic aberration: internal inverted DNA amplification with retention of the distal end of the chromosome. In this study, using yeast as a model, we test the feasibility of several of these steps for the formation of an inverted amplification: a specific DNA replication anomaly (1) leading to the formation of a palindromic extrachromosomal circular molecule (2) followed by the homologous reintegration of this molecule into the genome (3). A significant feature of this mode of amplification is that the amplified sequences contain one or more replication origins. The instability of the inverted junctions can lead, through homology driven processes, to more complex genomic structures that contain a partial triplication within a duplicated segment, a structure commonly found associated with human disease.
Collapse
Affiliation(s)
- Bonita J. Brewer
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Celia Payen
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Sara C. Di Rienzi
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Megan M. Higgins
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Giang Ong
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Maitreya J. Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - M. K. Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| |
Collapse
|
12
|
Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE. Conducting a microbiome study. Cell 2014; 158:250-262. [PMID: 25036628 DOI: 10.1016/j.cell.2014.06.037] [Citation(s) in RCA: 451] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/03/2014] [Accepted: 06/27/2014] [Indexed: 12/11/2022]
Abstract
Human microbiome research is an actively developing area of inquiry, with ramifications for our lifestyles, our interactions with microbes, and how we treat disease. Advances depend on carefully executed, controlled, and reproducible studies. Here, we provide a Primer for researchers from diverse disciplines interested in conducting microbiome research. We discuss factors to be considered in the design, execution, and data analysis of microbiome studies. These recommendations should help researchers to enter and contribute to this rapidly developing field.
Collapse
Affiliation(s)
- Julia K Goodrich
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Sara C Di Rienzi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Angela C Poole
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Omry Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - William A Walters
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - J Gregory Caporaso
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA; Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Ruth E Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
13
|
Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield JF, Ley RE. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife 2013; 2:e01102. [PMID: 24137540 PMCID: PMC3787301 DOI: 10.7554/elife.01102] [Citation(s) in RCA: 256] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/22/2013] [Indexed: 12/21/2022] Open
Abstract
Cyanobacteria were responsible for the oxygenation of the ancient atmosphere; however, the evolution of this phylum is enigmatic, as relatives have not been characterized. Here we use whole genome reconstruction of human fecal and subsurface aquifer metagenomic samples to obtain complete genomes for members of a new candidate phylum sibling to Cyanobacteria, for which we propose the designation 'Melainabacteria'. Metabolic analysis suggests that the ancestors to both lineages were non-photosynthetic, anaerobic, motile, and obligately fermentative. Cyanobacterial light sensing may have been facilitated by regulators present in the ancestor of these lineages. The subsurface organism has the capacity for nitrogen fixation using a nitrogenase distinct from that in Cyanobacteria, suggesting nitrogen fixation evolved separately in the two lineages. We hypothesize that Cyanobacteria split from Melainabacteria prior or due to the acquisition of oxygenic photosynthesis. Melainabacteria remained in anoxic zones and differentiated by niche adaptation, including for symbiosis in the mammalian gut. DOI:http://dx.doi.org/10.7554/eLife.01102.001.
Collapse
Affiliation(s)
- Sara C Di Rienzi
- Department of Microbiology, Cornell University, Ithaca, United States
| | - Itai Sharon
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Kelly C Wrighton
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Omry Koren
- Department of Microbiology, Cornell University, Ithaca, United States
| | - Laura A Hug
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
| | - Julia K Goodrich
- Department of Microbiology, Cornell University, Ithaca, United States
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, United States
| | - Ruth E Ley
- Department of Microbiology, Cornell University, Ithaca, United States
| |
Collapse
|
14
|
Abstract
Origins of replication present a paradox to evolutionary biologists. As a collection, they are absolutely essential genomic features, but individually are highly redundant and nonessential. It is therefore difficult to predict to what extent and in what regard origins are conserved over evolutionary time. Here, through a comparative genomic analysis of replication origins and chromosomal replication patterns in the budding yeasts Saccharomyces cerevisiae and Lachancea waltii, we assess to what extent replication origins survived genomic change produced from 150 million years of evolution. We find that L. waltii origins exhibit a core consensus sequence and nucleosome occupancy pattern highly similar to those of S. cerevisiae origins. We further observe that the overall progression of chromosomal replication is similar between L. waltii and S. cerevisiae. Nevertheless, few origins show evidence of being conserved in location between the two species. Among the conserved origins are those surrounding centromeres and adjacent to histone genes, suggesting that proximity to an origin may be important for their regulation. We conclude that, over evolutionary time, origins maintain sequence, structure, and regulation, but are continually being created and destroyed, with the result that their locations are generally not conserved.
Collapse
Affiliation(s)
- Sara C Di Rienzi
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | | | | | | | | | | |
Collapse
|
15
|
Di Rienzi SC, Lindstrom KC, Lancaster R, Rolczynski L, Raghuraman MK, Brewer BJ. Genetic, genomic, and molecular tools for studying the protoploid yeast, L. waltii. Yeast 2010; 28:137-51. [PMID: 21246627 DOI: 10.1002/yea.1826] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 09/17/2010] [Indexed: 11/11/2022] Open
Abstract
Sequencing of the yeast Kluyveromyces waltii (recently renamed Lachancea waltii) provided evidence of a whole genome duplication event in the lineage leading to the well-studied Saccharomyces cerevisiae. While comparative genomic analyses of these yeasts have proven to be extremely instructive in modeling the loss or maintenance of gene duplicates, experimental tests of the ramifications following such genome alterations remain difficult. To transform L. waltii from an organism of the computational comparative genomic literature into an organism of the functional comparative genomic literature, we have developed genetic, molecular and genomic tools for working with L. waltii. In particular, we have characterized basic properties of L. waltii (growth, ploidy, molecular karyotype, mating type and the sexual cycle), developed transformation, cell cycle arrest and synchronization protocols, and have created centromeric and non-centromeric vectors as well as a genome browser for L. waltii. We hope that these tools will be used by the community to follow up on the ideas generated by sequence data and lead to a greater understanding of eukaryotic biology and genome evolution.
Collapse
Affiliation(s)
- Sara C Di Rienzi
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA 98195, USA
| | | | | | | | | | | |
Collapse
|
16
|
Abstract
Genome rearrangements are mediators of evolution and disease. Such rearrangements are frequently bounded by transfer RNAs (tRNAs), transposable elements, and other repeated elements, suggesting a functional role for these elements in creating or repairing breakpoints. Though not well explored, there is evidence that origins of replication also colocalize with breakpoints. To investigate a potential correlation between breakpoints and origins, we analyzed evolutionary breakpoints defined between Saccharomyces cerevisiae and Kluyveromyces waltii and S. cerevisiae and a hypothetical ancestor of both yeasts, as well as breakpoints reported in the experimental literature. We find that origins correlate strongly with both evolutionary breakpoints and those described in the literature. Specifically, we find that origins firing earlier in S phase are more strongly correlated with breakpoints than are later-firing origins. Despite origins being located in genomic regions also bearing tRNAs and Ty elements, the correlation we observe between origins and breakpoints appears to be independent of these genomic features. This study lays the groundwork for understanding the mechanisms by which origins of replication may impact genome architecture and disease.
Collapse
|